Filtered Iterative Denoising for Linear Inverse Problems

Iterative denoising algorithms (IDAs) have been tremendously successful in a range of linear inverse problems arising in signal and image processing. The classic instance of this is the famous Iterative Soft-Thresholding Algorithm (ISTA), based on soft-thresholding of wavelet coefficients. More modern approaches to IDAs replace soft-thresholding with a black-box denoiser, such as BM3D or a learned deep neural network denoiser. These are often referred to as ``plug-and-play" (PnP) methods because, in principle, an off-the-shelf denoiser can be used for a variety of different inverse problems. The problem with PnP methods is that they may not provide the best solutions to a specific linear inverse problem; better solutions can often be obtained by a denoiser that is customized to the problem domain. A problem-specific denoiser, however, requires expensive re-engineering or re-learning which eliminates the simplicity and ease that makes PnP methods attractive in the first place. This paper proposes a new IDA that allows one to use a general, black-box denoiser more effectively via a simple linear filtering modification to the usual gradient update steps that accounts for the specific linear inverse problem. The proposed Filtered IDA (FIDA) is mathematically derived from the classical ISTA and wavelet denoising viewpoint. We show experimentally that FIDA can produce superior results compared to existing IDA methods with BM3D

Video feedback efficacy at Romig Middle School

Master's Project (M.Ed.) University of Alaska Fairbanks, 2019Romig Middle School in Anchorage, Alaska, is consistently ranked within the top ten most diverse middle schools in the nation. The main objective of this research will be to determine if video production students meet learning objectives better or worse with video feedback given. The secondary goal is to measure the efficacy of using video feedback as a delivery source of evaluation to students at the eighth-grade level. The methods involve pre-and-post class surveys on the feedback methods and quantitative data gathered on improved technique. The results of this research will guide the use of video feedback in video production classes and serve as a platform to expand video feedback delivery into technology classes

Validation and verification of the GeneFinder (TM) COVID-19 Plus RealAmp kit on the ELITe InGenius (R) instrument

Background: Throughout the SARS-CoV-2 pandemic, a rapid identification of the virus was essential to quickly recognize positive cases and limit further spread by applying appropriate infection prevention. Many diagnostic laboratories use a multiplex Real-Time PCR assay, as they are not only highly sensitive but also specific. Currently, there are several assays and platforms in the market available which target different SARS-CoV-2 genes. The aim of this study was to validate and verify the GeneFinder (TM) COVID-19 PLUS RealAmp kit on the ELITe InGenius (R) instrument and compare to the national reference method. Methods: GeneFinder (TM) COVID-19 PLUS RealAmp kit was evaluated against the routine WHO in- house RealTime PCR assay, which is also the national reference method in the Netherlands and used in our laboratory. The sensitivity was tested using the analytical panel from Qnostics (Glasgow, United Kingdom) and the specificity was tested with patient material comprising of other seasonal respiratory viruses. In addition, 96 clinical samples initially analyzed by routine Real-Time PCR were tested using the GeneFinder (TM) COVID-19 PLUS RealAmp kit on the ELITe InGenius (R) instrument. Results: The GeneFinder (TM) COVID-19 PLUS RealAmp kit had a similar performance compared to routine in-house testing, with a limit of detection of 500 dC/mL for the RdRp-gene and E gene. Meanwhile, the N gene showed a limit of detection of 50 dC/mL. The SARS-CoV-2 test was highly specific and detected no other respiratory viruses. The results of the clinical samples were comparable between both assays with similar Ct values observed for the in-house Real-Time-PCR and the GeneFinder (TM) COVID-19 PLUS RealAmp kit for the N gene. Conclusion: The GeneFinder (TM) COVID-19 PLUS RealAmp kit on the ELITe InGenius (R) instrument had an appropriate sensitivity and specificity that could be used in small scale laboratories or during night shifts where accurate diagnostics are crucial

Etude Clinique des niveaux de perturbation de la metacognition, de la cognition sociale et du contrôle exécutif dans la pathologie frontale

Recent and convergent studies in neuropsychology have suggested the importance of frontal regions to the integrity of a number of functions such as metamemory capacities, executive functions, and social skills (Theory of Mind : ToM). In this original work, following Stuss et Anderson (2004), we assume a link between disturbances of these functions. We proposed to 16 frontal patients and 20 matched healthy subjects a protocol designed to test metamemory, ToM and executive functions in order to analyze the relations between disturbances of self-awareness (metamemory) and awareness of others (ToM), and cognitive control (executive functions). Our results confirm the importance of frontal lobes on these capacities. No correlation was found between measures of metamemory, measures of ToM and executive scores. The observation of individual profiles emphasizes the existence of dissociations between self awareness and consciousness of the others, and between these two forms of metacognitive control and the executive functioning. These results confirm the importance to engage more studies combining aspects of ToM, metacognition and executive control, to better understand the organization and architecture of the functions supported by frontal lobe

Health-related quality of life and well-being in people over 75 years of age with end-stage kidney disease managed with dialysis or comprehensive conservative care: A cross-sectional study in the UK and Australia

© Author(s) (or their employer(s)) 2018. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ. Objective To measure health-related quality of life (HRQoL) and well-being in older people with end-stage kidney disease (ESKD) and to determine the association between treatment type and sociodemographic characteristics on these outcome measures. In addition, to assess the convergent validity between the HRQoL and well-being measure and their feasibility and acceptability in this population. Design Prospective cross-sectional study. Setting Three renal units in the UK and Australia. Participants 129 patients with ESKD managed with dialysis or with an estimated glomerular filtration ≤10 mL/min/1.73 m 2 and managed with comprehensive conservative, non-dialytic care. Outcome measures HRQoL and well-being were assessed using Short-Form six dimensions (SF-6D, 0-1 scale); Kidney Disease Quality of Life (KDQOL-36) (0-100 scale) and Investigating Choice Experiments Capability Measure-Older people (ICECAP-O, 0-1 scale). Linear regression assessed associations between treatment, HRQoL and well-being. Pearson's correlation coefficient assessed convergent validity between instruments. Results Median age of 81 years (IQR 78-85), 65% males; 83 (64%) were managed with dialysis and 46 (36%) with conservative care. When adjusted for treatment type and sociodemographic variables, those managed on dialysis reported lower mean SF-6D utility (-0.05, 95% CI-0.12 to 0.01); lower KDQOL Physical Component Summary score (-3.17, 95% CI-7.61 to 1.27); lower Mental Component Summary score (-2.41, 95% CI-7.66 to 2.84); lower quality of life due to burden (-28.59, 95% CI-41.77 to-15.42); symptoms (-5.93, 95% CI-14.61 to 2.73) and effects of kidney disease (-16.49, 95% CI-25.98 to-6.99) and lower overall ICECAP-O well-being (-0.07, 95% CI-0.16 to 0.02) than those managed conservatively. Correlation between ICECAP-O well-being and SF-6D utility scores was strong overall, 0.65 (

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud 510 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group I intron also carried a MITE sequence that, like the hupL MITE family, occurs broadly across the genome. The presence of a high degree of mobile elements in genes central to Thiomargarita's core metabolism has not been previously reported in free-living bacteria and suggests a highly mutable genome

Block of death-receptor apoptosis protects mouse cytomegalovirus from macrophages and is a determinant of virulence in immunodeficient hosts.

The inhibition of death-receptor apoptosis is a conserved viral function. The murine cytomegalovirus (MCMV) gene M36 is a sequence and functional homologue of the human cytomegalovirus gene UL36, and it encodes an inhibitor of apoptosis that binds to caspase-8, blocks downstream signaling and thus contributes to viral fitness in macrophages and in vivo. Here we show a direct link between the inability of mutants lacking the M36 gene (ΔM36) to inhibit apoptosis, poor viral growth in macrophage cell cultures and viral in vivo fitness and virulence. ΔM36 grew poorly in RAG1 knockout mice and in RAG/IL-2-receptor common gamma chain double knockout mice (RAGγC(-/-)), but the depletion of macrophages in either mouse strain rescued the growth of ΔM36 to almost wild-type levels. This was consistent with the observation that activated macrophages were sufficient to impair ΔM36 growth in vitro. Namely, spiking fibroblast cell cultures with activated macrophages had a suppressive effect on ΔM36 growth, which could be reverted by z-VAD-fmk, a chemical apoptosis inhibitor. TNFα from activated macrophages synergized with IFNγ in target cells to inhibit ΔM36 growth. Hence, our data show that poor ΔM36 growth in macrophages does not reflect a defect in tropism, but rather a defect in the suppression of antiviral mediators secreted by macrophages. To the best of our knowledge, this shows for the first time an immune evasion mechanism that protects MCMV selectively from the antiviral activity of macrophages, and thus critically contributes to viral pathogenicity in the immunocompromised host devoid of the adaptive immune system

Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells

DNA alterations in mitochondria are believed to play a role in carcinogenesis and are found in smoking-related cancers. We sought to replicate earlier findings for the association of smoking with increased mitochondrial DNA (mtDNA) content in buccal cells and further hypothesized that there would be an increased number of somatic mtDNA mutations in smokers. Buccal cells and blood lymphocytes were studied from 42 healthy smokers and 30 non-smokers. Temporal temperature gradient electrophoresis screening and sequencing was used to identify mtDNA mutations. The relative mtDNA content was determined by real-time polymerase chain reaction. Assuming that mtDNA in lymphocytes represents the inherited sequence, it was found that 31% of smokers harbored at least one somatic mtDNA mutation in buccal cells with a total of 39 point mutations and 8 short deletions/insertions. In contrast, only 23% of non-smokers possessed mutations with a total of 10 point mutations and no insertions/deletions detected. mtDNA somatic mutation density was higher in smokers (0.68/10 000 bp per person) than in non-smokers (0.2/10 000 bp per person). There was a statistically significant difference in the pattern of homoplasmy and heteroplasmy mutation changes between smokers and non-smokers. Whereas non-smokers had the most mutations in D-loop region (70%), smokers had mutations in both messenger RNA encoding gene (36%) and D-loop region (49%). The mean ratio of buccal cells to lymphocytes of mtDNA content in smokers was increased (2.81) when compared with non-smokers (0.46). These results indicate that cigarette smoke exposure affects mtDNA in buccal cells of smokers. Additional studies are needed to determine if mitochondrial mutation assays provide new or complementary information for estimating cigarette smoke exposure at the cellular level or as a cancer risk biomarker

Considerations on equity in management of end-stage kidney disease in low- and middle-income countries

Achievement of equity in health requires development of a health system in which everyone has a fair opportunity to attain their full health potential. The current, large country-level variation in the reported incidence and prevalence of treated end-stage kidney disease indicates the existence of system-level inequities. Equitable implementation of kidney replacement therapy (KRT) programs must address issues of availability, affordability, and acceptability. The major structural factors that impact equity in KRT in different countries are the organization of health systems, overall health care spending, funding and delivery models, and nature of KRT prioritization (transplantation, hemodialysis or peritoneal dialysis, and conservative care). Implementation of KRT programs has the potential to exacerbate inequity unless equity is deliberately addressed. In this review, we summarize discussions on equitable provision of KRT in low- and middle-income countries and suggest areas for future research