End-to-end Interpretable Learning of Non-blind Image Deblurring

Non-blind image deblurring is typically formulated as a linear least-squares problem regularized by natural priors on the corresponding sharp picture's gradients, which can be solved, for example, using a half-quadratic splitting method with Richardson fixed-point iterations for its least-squares updates and a proximal operator for the auxiliary variable updates. We propose to precondition the Richardson solver using approximate inverse filters of the (known) blur and natural image prior kernels. Using convolutions instead of a generic linear preconditioner allows extremely efficient parameter sharing across the image, and leads to significant gains in accuracy and/or speed compared to classical FFT and conjugate-gradient methods. More importantly, the proposed architecture is easily adapted to learning both the preconditioner and the proximal operator using CNN embeddings. This yields a simple and efficient algorithm for non-blind image deblurring which is fully interpretable, can be learned end to end, and whose accuracy matches or exceeds the state of the art, quite significantly, in the non-uniform case.Comment: Accepted at ECCV2020 (poster

Nonlinear Lattice Waves in Random Potentials

Localization of waves by disorder is a fundamental physical problem encompassing a diverse spectrum of theoretical, experimental and numerical studies in the context of metal-insulator transition, quantum Hall effect, light propagation in photonic crystals, and dynamics of ultra-cold atoms in optical arrays. Large intensity light can induce nonlinear response, ultracold atomic gases can be tuned into an interacting regime, which leads again to nonlinear wave equations on a mean field level. The interplay between disorder and nonlinearity, their localizing and delocalizing effects is currently an intriguing and challenging issue in the field. We will discuss recent advances in the dynamics of nonlinear lattice waves in random potentials. In the absence of nonlinear terms in the wave equations, Anderson localization is leading to a halt of wave packet spreading. Nonlinearity couples localized eigenstates and, potentially, enables spreading and destruction of Anderson localization due to nonintegrability, chaos and decoherence. The spreading process is characterized by universal subdiffusive laws due to nonlinear diffusion. We review extensive computational studies for one- and two-dimensional systems with tunable nonlinearity power. We also briefly discuss extensions to other cases where the linear wave equation features localization: Aubry-Andre localization with quasiperiodic potentials, Wannier-Stark localization with dc fields, and dynamical localization in momentum space with kicked rotors.Comment: 45 pages, 19 figure

Viability and Burden of Leishmania in Extralesional Sites during Human Dermal Leishmaniasis

Understanding of the dynamics and distribution of Leishmania in the human host is fundamental to the targeting of control measures and their evaluation. Amplification of parasite gene sequences in clinical samples from cutaneous leishmaniasis patients has provided evidence of Leishmania in blood, other tissues and sites distinct from the lesion and of persistence of infection after clinical resolution of disease. However, there is uncertainty about the interpretation of the presence of Leishmania DNA as indicative of viable parasites. Because RNA is short-lived and labile, its presence provides an indicator of viability. We amplified Leishmania 7SLRNA, a molecule involved in intracellular protein translocation, to establish viability and estimate parasite load in blood monocytes, tonsil swab samples, and tissue fluid from healthy skin of patients with dermal leishmaniasis. Results showed that during active dermal leishmaniasis, viable Leishmania are present in blood monocytes, tonsils and normal skin in quantities similar to that in lesions, demonstrating widespread dissemination of infection and subclinical involvement of tissues beyond the lesion site. Leishmania 7SLRNA will be useful in deciphering the role of human infection in transmission

Decrease of upper critical field with underdoping in cuprate superconductors

The transition temperature Tc of cuprate superconductors falls when the doping p is reduced below a certain optimal value. It is unclear whether this fall is due to strong phase fluctuations or to a decrease in the pairing gap. Different interpretations of photoemission data disagree on the evolution of the pairing gap and different estimates of the upper critical field Hc2 are in sharp contradiction. Here we resolve this contradiction by showing that superconducting fluctuations in the underdoped cuprate Eu-LSCO, measured via the Nernst effect, have a characteristic field scale that falls with underdoping. The critical field Hc2 dips at p = 0.11, showing that superconductivity is weak where stripe order is strong. In the archetypal cuprate superconductor YBCO, Hc2 extracted from other measurements has the same doping dependence, also with a minimum at p = 0.11, again where stripe order is present. We conclude that competing states such as stripe order weaken superconductivity and this, rather than phase fluctuations, causes Tc to fall as cuprates become underdoped.Comment: Supplementary Information file available upon request; Nature Physics (2012

A comparative genome-wide study of ncRNAs in trypanosomatids

<p>Abstract</p> <p>Background</p> <p>Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA) transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular regulation. With the availability of many whole genome sequences, comparative analysis has become a powerful tool to identify ncRNA molecules. In this study, we performed a systematic genome-wide in silico screen to search for novel small ncRNAs in the genome of <it>Trypanosoma brucei </it>using techniques of comparative genomics.</p> <p>Results</p> <p>In this study, we identified by comparative genomics, and validated by experimental analysis several novel ncRNAs that are conserved across multiple trypanosomatid genomes. When tested on known ncRNAs, our procedure was capable of finding almost half of the known repertoire through homology over six genomes, and about two-thirds of the known sequences were found in at least four genomes. After filtering, 72 conserved unannotated sequences in at least four genomes were found, 29 of which, ranging in size from 30 to 392 nts, were conserved in all six genomes. Fifty of the 72 candidates in the final set were chosen for experimental validation. Eighteen of the 50 (36%) were shown to be expressed, and for 11 of them a distinct expression product was detected, suggesting that they are short ncRNAs. Using functional experimental assays, five of the candidates were shown to be novel H/ACA and C/D snoRNAs; these included three sequences that appear as singletons in the genome, unlike previously identified snoRNA molecules that are found in clusters. The other candidates appear to be novel ncRNA molecules, and their function is, as yet, unknown.</p> <p>Conclusions</p> <p>Using comparative genomic techniques, we predicted 72 sequences as ncRNA candidates in <it>T. brucei</it>. The expression of 50 candidates was tested in laboratory experiments. This resulted in the discovery of 11 novel short ncRNAs in procyclic stage <it>T. brucei</it>, which have homologues in the other trypansomatids. A few of these molecules are snoRNAs, but most of them are novel ncRNA molecules. Based on this study, our analysis suggests that the total number of ncRNAs in trypanosomatids is in the range of several hundred.</p

Depletion of Trypanosome CTR9 Leads to Gene Expression Defects

The Paf complex of Opisthokonts and plants contains at least five subunits: Paf1, Cdc73, Rtf1, Ctr9, and Leo1. Mutations in, or loss of Paf complex subunits have been shown to cause defects in histone modification, mRNA polyadenylation, and transcription by RNA polymerase I and RNA polymerase II. We here investigated trypanosome CTR9, which is essential for trypanosome survival. The results of tandem affinity purification suggested that trypanosome CTR9 associates with homologues of Leo1 and Cdc73; genes encoding homologues of Rtf1 and Paf1 were not found. RNAi targeting CTR9 resulted in at least ten-fold decreases in 131 essential mRNAs: they included several that are required for gene expression and its control, such as those encoding subunits of RNA polymerases, exoribonucleases that target mRNA, RNA helicases and RNA-binding proteins. Simultaneously, some genes from regions subject to chromatin silencing were derepressed, possibly as a secondary effect of the loss of two proteins that are required for silencing, ISWI and NLP1

Dynamic modeling of the reactive twin-screw co-rotating extrusion process: experimental validation by using inlet glass fibers injection response and application to polymers degassing

International audienceIn this paper is described an original dynamic model of a reactive co-rotating twinscrew extrusion (TSE) process operated by the Rhodia company for the Nylon-66 degassing finishing step. In order to validate the model, dynamic experiments have been performed on a small-scale pilot plant. These experiments consist in a temporary injection of glass fibers at the inlet of the extruder after it has reached a given operating point. The outlet glass fibers mass fraction time variation is then measured. This experiment does not lead to the RTD measurement. As a matter of fact, due to the high quantity of glass fibers that is introduced, the behavior of the flow through the extruder is perturbed so that the glass fibers cannot be considered as an inert tracer. The dynamic model that we have published elsewhere (Choulak et al., Ind. Eng. Chem. Res., 2004, 43(23), 7373-7382) is adapted to take into account this nonlinear behavior of the extruder with respect to the glass fibers injection and is favorably compared to experimental results. The description of the degassing operation is also included in the model. The model allows simulations of the complete dynamic behavior of the process. When the steady state is reached, the good position of the degassing vent with respect to the partially and fully filled zones positions can also be checked, thus illustrating the way the model can be used for design purposes

Mechanical Strain Stabilizes Reconstituted Collagen Fibrils against Enzymatic Degradation by Mammalian Collagenase Matrix Metalloproteinase 8 (MMP-8)

Collagen, a triple-helical, self-organizing protein, is the predominant structural protein in mammals. It is found in bone, ligament, tendon, cartilage, intervertebral disc, skin, blood vessel, and cornea. We have recently postulated that fibrillar collagens (and their complementary enzymes) comprise the basis of a smart structural system which appears to support the retention of molecules in fibrils which are under tensile mechanical strain. The theory suggests that the mechanisms which drive the preferential accumulation of collagen in loaded tissue operate at the molecular level and are not solely cell-driven. The concept reduces control of matrix morphology to an interaction between molecules and the most relevant, physical, and persistent signal: mechanical strain.The investigation was carried out in an environmentally-controlled microbioreactor in which reconstituted type I collagen micronetworks were gently strained between micropipettes. The strained micronetworks were exposed to active matrix metalloproteinase 8 (MMP-8) and relative degradation rates for loaded and unloaded fibrils were tracked simultaneously using label-free differential interference contrast (DIC) imaging. It was found that applied tensile mechanical strain significantly increased degradation time of loaded fibrils compared to unloaded, paired controls. In many cases, strained fibrils were detectable long after unstrained fibrils were degraded.In this investigation we demonstrate for the first time that applied mechanical strain preferentially preserves collagen fibrils in the presence of a physiologically-important mammalian enzyme: MMP-8. These results have the potential to contribute to our understanding of many collagen matrix phenomena including development, adaptation, remodeling and disease. Additionally, tissue engineering could benefit from the ability to sculpt desired structures from physiologically compatible and mutable collagen

The impact of diabetes on the pathogenesis of sepsis

Diabetes is associated with an increased susceptibility to infection and sepsis. Conflicting data exist on whether the mortality of patients with sepsis is influenced by the presence of diabetes, fuelling the ongoing debate on the benefit of tight glucose regulation in patients with sepsis. The main reason for which diabetes predisposes to infection appears to be abnormalities of the host response, particularly in neutrophil chemotaxis, adhesion and intracellular killing, defects that have been attributed to the effect of hyperglycaemia. There is also evidence for defects in humoral immunity, and this may play a larger role than previously recognised. We review the literature on the immune response in diabetes and its potential contribution to the pathogenesis of sepsis. In addition, the effect of diabetes treatment on the immune response is discussed, with specific reference to insulin, metformin, sulphonylureas and thiazolidinediones

Effectiveness of manual therapies: the UK evidence report

<p>Abstract</p> <p>Background</p> <p>The purpose of this report is to provide a succinct but comprehensive summary of the scientific evidence regarding the effectiveness of manual treatment for the management of a variety of musculoskeletal and non-musculoskeletal conditions.</p> <p>Methods</p> <p>The conclusions are based on the results of systematic reviews of randomized clinical trials (RCTs), widely accepted and primarily UK and United States evidence-based clinical guidelines, plus the results of all RCTs not yet included in the first three categories. The strength/quality of the evidence regarding effectiveness was based on an adapted version of the grading system developed by the US Preventive Services Task Force and a study risk of bias assessment tool for the recent RCTs.</p> <p>Results</p> <p>By September 2009, 26 categories of conditions were located containing RCT evidence for the use of manual therapy: 13 musculoskeletal conditions, four types of chronic headache and nine non-musculoskeletal conditions. We identified 49 recent relevant systematic reviews and 16 evidence-based clinical guidelines plus an additional 46 RCTs not yet included in systematic reviews and guidelines.</p> <p>Additionally, brief references are made to other effective non-pharmacological, non-invasive physical treatments.</p> <p>Conclusions</p> <p>Spinal manipulation/mobilization is effective in adults for: acute, subacute, and chronic low back pain; migraine and cervicogenic headache; cervicogenic dizziness; manipulation/mobilization is effective for several extremity joint conditions; and thoracic manipulation/mobilization is effective for acute/subacute neck pain. The evidence is inconclusive for cervical manipulation/mobilization alone for neck pain of any duration, and for manipulation/mobilization for mid back pain, sciatica, tension-type headache, coccydynia, temporomandibular joint disorders, fibromyalgia, premenstrual syndrome, and pneumonia in older adults. Spinal manipulation is not effective for asthma and dysmenorrhea when compared to sham manipulation, or for Stage 1 hypertension when added to an antihypertensive diet. In children, the evidence is inconclusive regarding the effectiveness for otitis media and enuresis, and it is not effective for infantile colic and asthma when compared to sham manipulation.</p> <p>Massage is effective in adults for chronic low back pain and chronic neck pain. The evidence is inconclusive for knee osteoarthritis, fibromyalgia, myofascial pain syndrome, migraine headache, and premenstrual syndrome. In children, the evidence is inconclusive for asthma and infantile colic.</p