Evaluation of non-commercial models for genotoxicity and carcinogenicity in the assessment of EFSA's databases.

Over the past years, the European Food Safety Authority (EFSA) released to the public domain several databases, with the main objectives of collecting and storing hazard data on the substances considered in EFSA's risk assessment and secondly to serve as a basis for further development of in silico tools such as quantitative structure-activity relationship (QSAR) models. In this work, we evaluated the ability of freely available QSAR models to estimate genotoxicity and carcinogenicity properties and their possible use for screening purposes on three different EFSA's databases. With an accuracy close to 90%, the results showed good capabilities of QSAR models to predict genotoxicity in terms of bacterial reverse mutation test, while statistics for in vivo micronucleus test are not satisfactory (accuracy in the predictions close to 50%). Interestingly, results on the carcinogenicity assessment showed an accuracy in prediction close to 70% for the best models. In addition, an example of the potential application of in silico models is presented in order to provide a preliminary screening of genotoxicity properties of botanicals intended for use as food supplements.

Could deep learning in neural networks improve the QSAR models?

Assessing chemical toxicity is a multidisciplinary process, traditionally involving in vivo, in vitro and in silico tests. Currently, toxicological goal is to reduce new tests on chemicals, exploiting all information yet available. Recent advancements in machine learning and deep neural networks allow computers to automatically mine patterns and learn from data. This technology, applied to (Q)SAR model development, leads to discover by learning the structural-chemical-biological relationships and the emergent properties. Starting from Toxception, a deep neural network predicting activity from the chemical graph image, we designed SmilesNet, a recurrent neural network taking SMILES as the only input. We then integrated the two networks into C-Tox network to make the final classification. Results of our networks, trained on a ~20K molecule dataset with Ames test experimental values, match or even outperform the current state of the art. We also extract knowledge from the networks and compare it with the available mutagenic structural alerts. The advantage over traditional QSAR modelling is that our models automatically extract the features without using descriptors. Nevertheless, the model is successful if large numbers of examples are provided and computation is more complex than in classical methods.

Dynamic membrane patterning, signal localization and polarity in living cells.

We review the molecular and physical aspects of the dynamic localization of signaling molecules on the plasma membranes of living cells. At the nanoscale, clusters of receptors and signaling proteins play an essential role in the processing of extracellular signals. At the microscale, "soft" and highly dynamic signaling domains control the interaction of individual cells with their environment. At the multicellular scale, individual polarity patterns control the forces that shape multicellular aggregates and tissues.

Laser removal of tattoos.

In Western countries the phenomenon of "tattooing" is expanding and tattoos are considered a new fashion among young people. In this paper we briefly trace the history of tattooing, the techniques used, the analysis of pigments used, and their possible adverse reactions. We also carried out a review of the international literature on the use of Q-switched laser in tattoo removal and its complications, and we describe our experience in the use of this technique.

Ehlers-Danlos syndrome: case report and an electron microscopy study.

Ehlers-Danlos syndrome (EDS) type III is a inherited connective tissue disorders characterized by extensibility of the skin, hypermobility of the joints, chronic pain, tissue fragility, easy bruising, and delayed wound healing with result of atrophic scars. The patients report commonly a history of recurrent dislocations of the shoulders and knees after low-impact trauma, chronic joint pain, and early osteoarthritis, which lead to diagnosis. The pathogenesis of this condition is unknown, and the diagnosis is generally made in adult age, based only on clinical criteria. In this report, we describe a case of a 50-year-old woman with a 30-year history of recurrent dislocations and atrophic scars. We performed diagnosis of EDS type III after a complete clinical and instrumental evaluation, comprising of histological and electron microscopic studies, that highlighted collagen abnormalities.

Epilepsy and argininosuccinic aciduria.

BACKGROUND: We have reviewed the occurrence of epilepsy in our patients with argininosuccinic aciduria (ASA) (OMIM 207900) and the possible relationship of late epilepsy to symptomatic seizures in the neonatal period, hyperammonaemia and treatments. METHODS: We retrospectively analysed 11 ASA patients (8 neonatal onset and 3 late onset), 6 of whom had developed epilepsy. RESULTS: Epilepsy in our sample was frequent (55 %). It developed after a seizure-free period from the onset of the metabolic disease and seizures were responsive to treatment in all cases. Arginine plasma levels were kept in the same range for the 2 groups of patients with and without epilepsy. CONCLUSIONS: Although epilepsy is reported to be common among patients with ASA, very few long-term follow-up studies are available. The pathophysiological mechanism of epileptogenesis remains unclear. Neither hyperammonaemia nor acute symptomatic seizures at birth seem to be predictive of late epilepsy. Excessive arginine dosages as a cause of epilepsy could be reasonably excluded since our 3 late onset patients developed epilepsy before the diagnosis of ASA, at a time when they were likely to be arginine deficient. Arginine deficiency may not be excluded as cause of epilepsy, but further studies are needed to define its role.

Mitral valve prolapse and abnormalities of haemostasis in children and adolescents with migraine with aura and other idiopathic headaches: a pilot study.

OBJECTIVE: To investigate the prevalence of mitral valve prolapse (MVP) and abnormalities of haemostasis in children and adolescents with migraine with aura (MA) compared with peers affected by other idiopathic headaches. MATERIALS AND METHODS: We recruited 20 MA patients (10 men and 10 women; age range 8-17 years) and 20 sex- and age-matched subjects with other idiopathic headaches. Both groups underwent colour Doppler transthoracic echocardiography to detect MVP and the following laboratory work-up: plasma prothrombin time, activated partial thromboplastin time, thrombin time, fibrinogen, protein C, protein S, homocysteine, lupus anticoagulant, von Willebrand factor (vWF) ristocetin cofactor activity, immunoglobulins (Ig) G and M anticardiolipin antibodies (aCL). Factor V Leiden, factor II and methylenetetrahydrofolate reductase were investigated (we did not test the entire genes, but screened for specific point mutations). RESULTS: The prevalence of MVP was significantly higher in the MA subjects than in the patients affected by other idiopathic headaches (40% vs 10%; P < 0.05). Moreover, the MA patients showed a higher rate of above-normal IgM aCL titres (45% vs 10%; P < 0.05). Finally, in the group of patients with MVP we found a higher prevalence of aCL in those with MA compared with those affected by other idiopathic headaches. CONCLUSIONS: A proportion, at least, of the MA patients showed a more complex phenotype characterized by MVP and/or positive aCL titres. The pathogenetic role of these associations is obscure and larger studies are needed to confirm the usefulness of echocardiographic and laboratory investigations in this area and to identify possible new treatment approaches that might be explored in this group of MA patients.

Insulin-degrading enzyme: structure-function relationship and its possible roles in health and disease.

Insulin-degrading enzyme (IDE) or insulysin is a highly conserved Zn(2+) -dependent endopeptidase with an "inverted" HxxEH motif. In vivo, IDE contributes to regulate the steady state levels of peripheral insulin and cerebral amyloid beta peptide (Abeta) of Alzheimer's disease. In vitro, substrates of IDE include a broad spectrum of peptides with relevant physiological functions such as atrial natriuretic factor, insulin-like growth factor-II, transforming growth factor-alpha, beta-endorphin, amylin or glucagon. The recently solved crystal structures of an inactive IDE mutant bound to four different substrates indicate, in accordance with previous compelling biochemical data, that peptide backbone conformation and size are major determinants of IDE recognition and substrate selectivity. IDE-N and IDE-C halves contribute to substrate binding and may rotate away from each other leading to open and closed conformers that permit or preclude the entry of substrates. Noteworthy, stabilization of substrate beta strands in their IDE-bound form may explain the preference of IDE for peptides with a high tendency to self-assembly as amyloid fibrils. These structural requirements may underlie the capability of some amyloid peptides of forming extremely stable complexes with IDE and raise the possibility of a dead-end chaperone-like function of IDE independent of catalysis. Furthermore, the recent recognition of IDE as a varicella zoster virus receptor and its putative involvement in muscle cell differentiation, steroid receptor signaling or proteasome modulation suggest that IDE is a multi-functional protein with broad and relevant roles in several basic cellular processes. Accordingly, IDE functions, regulation or trafficking may partake in the molecular pathogenesis of major human diseases and become potential targets for therapeutic intervention.

Symmetry breaking mechanism for epithelial cell polarization.

In multicellular organisms, epithelial cells form layers separating compartments responsible for different physiological functions. At the early stage of epithelial layer formation, each cell of an aggregate defines an inner and an outer side by breaking the symmetry of its initial state, in a process known as epithelial polarization. By integrating recent biochemical and biophysical data with stochastic simulations of the relevant reaction-diffusion system, we provide evidence that epithelial cell polarization is a chemical phase-separation process induced by a local bistability in the signaling network at the level of the cell membrane. The early symmetry breaking event triggering phase separation is induced by adhesion-dependent mechanical forces localized in the point of convergence of cell surfaces when a threshold number of confluent cells is reached. The generality of the emerging phase-separation scenario is likely common to many processes of cell polarity formation.

Outcome of patients listed for heart transplantation after a failed surgical ventricular restoration procedure.

Patients with end-stage ischemic cardiomyopathy (IHD) and left ventricular (LV) dilatation are increasingly treated by means of surgical ventricular restoration (SVR). In some patients, SVR can delay heart transplantation (HTX). We retrospectively analyzed our experience, trying to ascertain whether HTX after a failed SVR (fSVR) carried a greater mortality risk. Since 1985, we performed 742 HTX. Since June 1999, 133 IHD patients were listed for HTX. We assigned them to 3 groups: (A) not a redo (n=54); (B) redo after coronary artery bypass grafting (n=54); and (C) redo after fSVR (n=25). Respectively, 37, 33, and 12 patients underwent HTX with in-hospital mortality after HTX of 4/37 (10.8%), 12/33 (36.4%), and 2/12 (16.7%). Mortality on the list was 9/54 (16.7%), 11/54 (20.4%), and 7/25 (28.0%) respectively. Removal from the list occurred in 4, 5, and 2 patients, and 4, 5, and 4 patients are still awaiting HTX, respectively. In group C, the mean time from SVR to HTX list was 45.6+/-43.3 months, and list mortality occurred after 5.83+/-5.81 months. In-hospital mortality in both patients of group C was due to the occurrence of multisystem organ failure; 10/12 were extubated after 19.3+/-9.6 hours and discharged from the intensive care unit after 3.9+/-1.6 days. The recorded complications were: 3 acute renal failure, 1 pericardial effusion, and 2 episodes of acute rejection. Since only 5/25 patients with fSVR had undergone SVR at our institution, we cannot establish which patients were really eligible for HTX at the time of SVR. Our experience showed that patients listed for HTX displayed a high list mortality, but that HTX after a failed SVR did not seem to have a poorer outcome than HTX after previous conventional CABG.

Patch coalescence as a mechanism for eukaryotic directional sensing.

Eukaryotic cells possess a sensible chemical compass allowing them to orient toward sources of soluble chemicals. The extracellular chemical signal triggers separation of the cell membrane into two domains populated by different phospholipid molecules and oriented along the signal anisotropy. We propose a theory of this polarization process, which is articulated into subsequent stages of germ nucleation, patch coarsening, and merging into a single domain. We find that the polarization time, t{epsilon}, depends on the anisotropy degree through the power law t{epsilon} infinity epsilon{-2}, and that in a cell of radius R there should exist a threshold value epsilon{th} infinity R{-1} for the smallest detectable anisotropy.

Possible role of everolimus in improving renal function in long-term heart transplantation.

Patient survival after heart transplantation has improved dramatically since the availability of calcineurine inhibitor (CNIs); the number of long-term patients is progressively increasing. However, in these patients, nephrotoxicity of CNIs has been largely responsible for the progressive development of renal dysfunction. Since impaired renal function is an important issue that reduces long-term patient survival, it is important to develop strategies to improve renal function while maintaining immunologic safety to preserve graft function. Everolimus is an mTOR inhibitor sirolimus analogue, that has proved, to be highly efficacious to prevent acute myocardial rejection and reduce the severity of cardiac allograft vasculopathy in de novo HTx patients. There is reasonable evidence that, in long term heart transplanted patients, renal function may improve when everolimus is administered associated with a progressive reduction of CNIs. So far there is no evidence to identify which patient may benefit from this therapeutic approach. Indeed everolimus alone may be equally effective to prevent rejection and improve renal function when CNIs are completely discontinued, but data are still lacking on the risks, dosages and side effects of this type of immunosuppression. Ongoing clinical studies will provide further guidance about the possibility to halt or reduce the progression of renal impairment in long term heart transplant patients.

Atrial natriuretic peptide in diabetic and nondiabetic patients with and without heart transplantation.

BACKGROUND: Natriuretic peptides are useful markers for risk stratification of patients with heart disease. However, conflicting results have been reported about circulating atrial natriuretic peptide (ANP) concentration in heart transplant recipients. METHODS: To ascertain the effects of diabetes and acute insulin administration on plasma ANP concentrations in a model of heart denervation, we studied 12 diabetic (D-OHT) and 6 nondiabetic heart-transplanted (OHT) patients using the euglycemic-hyperinsulinemic clamp and oral glucose tolerance tests. Five patients with type 2 diabetes without heart transplantation (D) and 9 healthy subjects (NOR) matched for anthropometric features served as the controls. RESULTS: Means baseline plasma ANP concentration was higher in D-OHT (82 +/- 15 pg/mL) than in OHT or NOR (27 +/- 4 or 30 +/- 5; P < .01), but was not different than D (69 +/- 12; P = .82). During the clamp plasma ANP showed similar increases in all groups (49 +/- 4, 39 +/- 3, 59 +/- 4, and 49 +/- 3% in D-OHT, OHT, D, and NOR; P < .02 vs basal, P = NS among groups). Plasma osmolarity and catecholamines were also not different among groups and did not increase during the clamp. Fasting plasma ANP concentrations correlated with plasma glucose concentrations measured 120 minutes after oral glucose tolerance testing. CONCLUSIONS: Among heart transplantation recipients fasting plasma ANP concentrations were not different at 5 to 6 years after the surgical procedure than in nondiabetic controls. Increased ANP concentrations were observed among recipients with diabetes and among nontransplanted diabetic patients. Although the insulin-induced increment in ANP concentrations was not different among groups, circulating ANP was strongly associated with glucose tolerance status.

Role of repulsive factors in vascularization dynamics.

Capillary networks are essential in vertebrates to supply tissues with nutrients. Experiments of in vitro capillary formation show that endothelial cells randomly spread on a gel matrix autonomously organize to form vascular networks with a characteristic length independent of the initial cell density. A mathematical model based on free cell migration and on cell cross-talk mediated by soluble chemical factors has been recently proposed and explains the main dynamical and geometrical properties of the networks. We extend this model introducing the action of repulsive factors and we show that their activity results in a larger degree of reorganization of cellular matter and in more robust control over the size of the growing vascular network.

Cell directional persistence [corrected] and chemotaxis in vascular morphogenesis.

In vertebrates, supply of oxygen and nutrients to tissues is carried out by the blood vascular system through capillary networks. Capillary patterns are closely mimicked by endothelial cells cultured on Matrigel, a preparation of basement membrane proteins. On the Matrigel surface, single randomly dispersed endothelial cells self-organize into vascular networks. The network is characterized by a typical length scale, which is independent of the initial mean density of deposed cells n over a wide range of values of n. We give here a detailed description of a mathematical model of the process which is able to reproduce several qualitative and quantitative features of in vitro vascularization experiments. Cell matter is basically modelled as an elastic fluid subjected to a specific force field depending on the concentration of a chemoattractant factor. Starting from sparse initial data, mimicking the initial conditions realized in laboratory experiments, numerical solutions reproduce characteristic network structures, similar to observed ones, whose average size is theoretically related to the finite range of chemoattractant diffusion. A possible area of application of the model is the design of properly vascularized artificial tissues.

Percolation and Burgers' dynamics in a model of capillary formation.

Capillary networks are essential in vertebrates to supply tissues with nutrients. Experiments of in vitro capillary formation show that cells randomly spread on a gel matrix autonomously organize to form vascular networks. Cells form disconnected networks at low densities and connected ones above a critical density. Above the critical density the network is characterized by a typical mesh size approximately 200 microm, which is approximately constant on a wide range of density values. In this paper we present a full characterization of a recently proposed model which reproduces the main features of the biological system, focusing on its dynamical properties, on the fractal properties of patterns, and on the percolative phase transition. We discuss the relevance of the model in relation with some experiments in living beings and proposed diagnostic methods based on the measurement of the fractal dimension of vascular networks.

Percolation, morphogenesis, and burgers dynamics in blood vessels formation.

Experiments of in vitro formation of blood vessels show that cells randomly spread on a gel matrix autonomously organize to form a connected vascular network. We propose a simple model which reproduces many features of the biological system. We show that both the model and the real system exhibit a fractal behavior at small scales, due to the process of migration and dynamical aggregation, followed at large scale by a random percolation behavior due to the coalescence of aggregates. The results are in good agreement with the analysis performed on the experimental data.