Limited-memory scaled gradient projection methods for real-time image deconvolution in microscopy

Gradient projection methods have given rise to effective tools for image deconvolution in several relevant areas, such as microscopy, medical imaging and astronomy. Due to the large scale of the optimization problems arising in nowadays imaging applications and to the growing request of real-time reconstructions, an interesting challenge to be faced consists in designing new acceleration techniques for the gradient schemes, able to preserve the simplicity and low computational cost of each iteration. In this work we propose an acceleration strategy for a state of the art scaled gradient projection method for image deconvolution in microscopy. The acceleration idea is derived by adapting a step-length selection rule, recently introduced for limited-memory steepest descent methods in unconstrained optimization, to the special constrained optimization framework arising in image reconstruction. We describe how important issues related to the generalization of the step-length rule to the imaging optimization problem have been faced and we evaluate the improvements due to the acceleration strategy by numerical experiments on large-scale image deconvolution problems

A case report of a rare intramuscular granular cell tumor

Background: Granular cell tumors (GCTs) were firstly described by Weber in 1854 and 70 years later by Abrikossoff and classified as benign tumors. Originally considered muscle tumors, they have been identified as neural lesions, due to their close association with nerve and to their immunohystochemical characteristics. GCTs are uncommon tumors and they may arise in any part of the body; they have been mainly observed in tongue, chest wall and upper extremities; less frequent sites are larynx, gastrointestinal tract, breast, pituitary stalk and the female anogenital region. Here we report a case of GCT showing an uncommon localization such as the upper third of the right rectus muscle of the abdominal wall. Case presentation: A 45 year-old woman of Caucasian origin presented to the surgeon with a 6-month history of light pain in the upper third of the abdominal wall. Radiological exams (Ultrasonography, Computed Tomography and Contrast magnetic resonance imaging) showed a localized in the right rectus abdominis muscle. After excision, histological and immunohystochemical analysis, with the support of electron microscopy, allowed making diagnosis of granular cell tumor. Discussion: After fist description by Abrikosoff in 1926 of GCT like mesenchymal tumor of unknown origin, in recent years immunohystochemical techniques definitely demonstrated the histogenetic derivation of GCT from Schwann cells. Granular cell tumors are rare, small, slow-growing, solitary and painless subcutaneous nodules which behave in a benign fashion, but can have a tendency to recur; in rare cases they can metastasize, when they became malignant; there are some clinical and histological criteria to suspect the malignance of this tumor. Conclusion: It is important that clinicians, radiologists and pathologists are aware of the clinical presentation and histopathology of GCT for appropriate management, counselling and follow-up. In our case we had a complete radiological, morphological and immunohystochemical characterization of the lesion and a definitive diagnosis of benignity confirmed by electron microscopy

AQP1 Is Not Only a Water Channel: It Contributes to Cell Migration through Lin7/Beta-Catenin

Background: AQP1 belongs to aquaporins family, water-specific, membrane-channel proteins expressed in diverse tissues. Recent papers showed that during angiogenesis, AQP1 is expressed preferentially by microvessels, favoring angiogenesis via the increase of permeability In particular, in AQP1 null mice, endothelial cell migration is impaired without altering their proliferation or adhesion. Therefore, AQP1 has been proposed as a novel promoter of tumor angiogenesis. Methods/Findings: Using targeted silencing of AQP1 gene expression, an impairment in the organization of F-actin and a reduced migration capacity was demonstrated in human endothelial and melanoma cell lines. Interestingly, we showed, for the first time, that AQP1 co-immunoprecipitated with Lin-7. Lin7-GFP experiments confirmed co-immunoprecipitation. In addition, the knock down of AQP1 decreased the level of expression of Lin-7 and b-catenin and the inhibition of proteasome contrasted partially such a decrease. Conclusions/Significance: All together, our findings show that AQP1 plays a role inside the cells through Lin-7/b-catenin interaction. Such a role of AQP1 is the same in human melanoma and endothelial cells, suggesting that AQP1 plays a global physiological role. A model is presented

Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.This work was supported in part by grant “Progetto di Ateneo PRAT CPDA154841/15” from the University of Padova

Comparison of discretization strategies for the model-free information-theoretic assessment of short-term physiological interactions

This work presents a comparison between different approaches for the model-free estimation of information-theoretic measures of the dynamic coupling between short realizations of random processes. The measures considered are the mutual information rate (MIR) between two random processes X and Y and the terms of its decomposition evidencing either the individual entropy rates of X and Y and their joint entropy rate, or the transfer entropies from X to Y and from Y to X and the instantaneous information shared by X and Y. All measures are estimated through discretization of the random variables forming the processes, performed either via uniform quantization (binning approach) or rank ordering (permutation approach). The binning and permutation approaches are compared on simulations of two coupled non-identical Hènon systems and on three datasets, including short realizations of cardiorespiratory (CR, heart period and respiration flow), cardiovascular (CV, heart period and systolic arterial pressure), and cerebrovascular (CB, mean arterial pressure and cerebral blood flow velocity) measured in different physiological conditions, i.e., spontaneous vs paced breathing or supine vs upright positions. Our results show that, with careful selection of the estimation parameters (i.e., the embedding dimension and the number of quantization levels for the binning approach), meaningful patterns of the MIR and of its components can be achieved in the analyzed systems. On physiological time series, we found that paced breathing at slow breathing rates induces less complex and more coupled CR dynamics, while postural stress leads to unbalancing of CV interactions with prevalent baroreflex coupling and to less complex pressure dynamics with preserved CB interactions. These results are better highlighted by the permutation approach, thanks to its more parsimonious representation of the discretized dynamic patterns, which allows one to explore interactions with longer memory while limiting the curse of dimensionality

Draft genome sequence of the nitrogen-fixing Rhizobium sullae type strain IS123^T focusing on the key genes for symbiosis with its host Hedysarum coronarium L.

© 2017 Sablok, Rosselli, Seeman, van Velzen, Polone, Giacomini, La Porta, Geurts, Muresu and Squartini. The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123T nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592), to two congeneric cases (Rhizobium leguminosarum bv. viciae and Rhizobium etli) and up to different genera within the legume-nodulating taxa. The host plant is of agricultural importance, but, unlike the majority of other domesticated plant species, it is able to survive quite well in the wild. Data showed that that the type strain of R. sullae, isolated from a wild host specimen, is endowed with a richer array of symbiotic genes in comparison to other strains, species or genera of rhizobia that were rescued from domesticated plant ecotypes. The analysis revealed that the bacterium by itself is incapable of surviving in the extreme conditions that its host plant can tolerate. When exposed to drought or alkaline condition, the bacterium depends on its host to survive. Data are consistent with the view of the plant phenotype as the primary factor enabling symbiotic nitrogen fixing bacteria to survive in otherwise limiting environments

Disentangling cardiovascular control mechanisms during head-down tilt via joint transfer entropy and self-entropy decompositions

A full decomposition of the predictive entropy (PE) of the spontaneous variations of the heart period (HP) given systolic arterial pressure (SAP) and respiration (R) is proposed. The PE of HP is decomposed into the joint transfer entropy (JTE) from SAP and R to HP and self-entropy (SE) of HP. The SE is the sum of three terms quantifying the synergistic/redundant contributions of HP and SAP, when taken individually and jointly, to SE and one term conditioned on HP and SAP denoted as the conditional SE (CSE) of HP given SAP and R. The JTE from SAP and R to HP is the sum of two terms attributable to SAP or R plus an extra term describing the redundant/synergistic contribution to the JTE. All quantities were computed during cardiopulmonary loading induced by -25\uc2\ub0 head-down tilt (HDT) via a multivariate linear regression approach. We found that: (i) the PE of HP decreases during HDT; (ii) the decrease of PE is attributable to a lessening of SE of HP, while the JTE from SAP and R to HP remains constant; (iii) the SE of HP is dominant over the JTE from SAP and R to HP and the CSE of HP given SAP and R is prevailing over the SE of HP due to SAP and R both in supine position and during HDT; (iv) all terms of the decompositions of JTE from SAP and R to HP and SE of HP due to SAP and R were not affected by HDT; (v) the decrease of the SE of HP during HDT was attributed to the reduction of the CSE of HP given SAP and R; (vi) redundancy of SAP and R is prevailing over synergy in the information transferred into HP both in supine position and during HDT, while in the HP information storage synergy and redundancy are more balanced. The approach suggests that the larger complexity of the cardiac control during HDT is unrelated to the baroreflex control and cardiopulmonary reflexes and may be related to central commands and/or modifications of the dynamical properties of the sinus node

A New Framework for the Time- and Frequency-Domain Assessment of High-Order Interactions in Networks of Random Processes

While the standard network description of complex systems is based on quantifying the link between pairs of system units, higher-order interactions (HOIs) involving three or more units often play a major role in governing the collective network behavior. This work introduces a new approach to quantify pairwise and HOIs for multivariate rhythmic processes interacting across multiple time scales. We define the so-called O-information rate (OIR) as a new metric to assess HOIs for multivariate time series, and present a framework to decompose the OIR into measures quantifying Granger-causal and instantaneous influences, as well as to expand all measures in the frequency domain. The framework exploits the spectral representation of vector autoregressive and state space models to assess the synergistic and redundant interaction among groups of processes, both in specific bands of interest and in the time domain after whole-band integration. Validation of the framework on simulated networks illustrates how the spectral OIR can highlight redundant and synergistic HOIs emerging at specific frequencies, which cannot be detected using time-domain measures. The applications to physiological networks described by heart period, arterial pressure and respiration variability measured in healthy subjects during a protocol of paced breathing, and to brain networks described by electrocorticographic signals acquired in an animal experiment during anesthesia, document the capability of our approach to identify informational circuits relevant to well-defined cardiovascular oscillations and brain rhythms and related to specific physiological mechanisms involving autonomic control and altered consciousness. The proposed framework allows a hierarchically-organized evaluation of timeand frequency-domain interactions in dynamic networks mapped by multivariate time series, and its high flexibility and scalability make it suitable for the investigation of networks beyond pairwise interactions in neuroscience, physiology and many other fields

Characterization of Removable Coatings for Graphite-moderated Nuclear Reactors Decommissioning

In this study the behavior and characteristics of two removable coatings to be deposited on a nuclear grade graphite substrate were analyzed, with the aim to evaluate their possible application on graphite bricks during dismantling operations of graphite-moderated nuclear reactors.Indeed, nowadays many shut-down reactors are still in decommissioning phase, and effective measures should be taken to guarantee safe dismantling operations. One option could be the use of coating application techniques, which mitigate the risk of graphite dusts spreading and loose contamination, protecting clean surfaces.Tested coatings, both polymeric mixtures, were selected according to their previous application history, availability in commerce and easiness in handling, whereas substrates used were non-irradiated nuclear Virgin Atcheson Graphite Ordinary Temperature (AGOT) graphite samples from L-54M Politecnico di Milano research reactor, which is in decommissioning phase. Thermal characterization of the coatings was carried out before deposition using a Thermogravimetric and Differential Thermal Analysis (TGA-DTA) equipment, tests were performed to obtain a preliminary estimation of the drying time and degradation conditions. After deposition, mechanical properties, such as hardness, of the coating were assessed. The preliminary experimental campaign showed that coating painting could be a feasible option to prevent the spread of highly contaminated graphite dusts during decommissioning of graphite components of nuclear reactors, thus ensuring clean and safe working conditions

Significance of serum Myostatin in hemodialysis patients

Background: Malnutrition and muscle wasting are common in haemodialysis (HD) patients. Their pathogenesis is complex and involves many molecules including Myostatin (Mstn), which acts as a negative regulator of skeletal muscle. The characterisation of Mstn as a biomarker of malnutrition could be useful in the prevention and management of this condition. Previous studies have reported no conclusive results on the actual relationship between serum Mstn and wasting and malnutrition. So, in this study, we evaluated Mstn profile in a cohort of regular HD patients. Methods: We performed a cross-sectional study, enrolling 37 patients undergoing bicarbonate-HD (BHD) or haemodiafiltration (HDF) at least for six months. 20 sex-matched healthy subjects comprised the control group. Mstn serum levels were evaluated by ELISA before and after HD. We collected clinical and biochemical data, evaluated insulin resistance, body composition, malnutrition [by Malnutrition Inflammation Score (MIS)] and tested muscle function (by hand-grip strength, six-minute walking test and a questionnaire on fatigue). Results: Mstn levels were not significantly different between HD patients and controls (4.7 \ub1 2.8 vs 4.5 \ub1 1.3 ng/ml). In addition, while a decrease in Mstn was observed after HD treatment, there were no differences between BHD and HDF. In whole group of HD patients Mstn was positively correlated with muscle mass (r = 0.82, p < 0.001) and inversely correlated with age (r = - 0.63, p < 0.01) and MIS (r = - 0.39, p = 0.01). No correlations were found between Mstn and insulin resistance, such as between Mstn levels and parameters of muscle strength and fatigue. In multivariate analysis, Mstn resulted inversely correlated with fat body content (\u3b2 = - 1.055, p = 0.002). Conclusions: Circulating Mstn is related to muscle mass and nutritional status in HD patients, suggesting that it may have a role in the regulation of skeletal muscle and metabolic processes. However, also considering the lack of difference of serum Mstn between healthy controls and HD patients and the absence of correlations with muscle function tests, our findings do not support the use of circulating Mstn as a biomarker of muscle wasting and malnutrition in HD