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1.  Complex network theory and the brain 
doi:10.1098/rstb.2013.0520
PMCID: PMC4150297  PMID: 25180300
topology; graph; connectome; neuroimaging; hubs; community structure
2.  A new family with hereditary lysozyme amyloidosis with gastritis and inflammatory bowel disease as prevailing symptoms 
BMC Gastroenterology  2014;14(1):159.
Background
Systemic amyloidoses is a heterogeneous group of diseases either acquired or hereditary. Amyloidoses can involve the gastrointestinal tract and the nature of the precursor protein that forms the fibrils deposits should be identified to adjust the treatment and evaluate the prognosis. Lysozyme amyloidosis (ALys) is a rare, systemic non neuropathic hereditary amyloidosis with a heterogenous phenotype including gastrointestinal, renal and hepatic symptoms.
Case presentation
We report and describe symptoms and gastrointestinal tract involvement in a new family with hereditary lysozyme amyloidosis. Clinical manifestations and organ involvement of nine affected members of a new family with the p.Trp82Arg ALys variant were recorded. All affected individuals suffered with prevailing gastrointestinal symptoms leading to the diagnosis of ALys. 8/9 had non specific upper gastrointestinal symptoms and 3/9 had rectocolic inflammation evoking inflammatory bowel disease. No other organ involvement by amyloidosis was found. Histological examination revealed amyloid deposits in all cases and all carried the p.Trp82Arg ALys variant at a heterozygous state.
Conclusion
Hereditary amyloidosis associated with the p.Trp82Arg lysozyme variant in this new family is predominantly associated with mild upper gastrointestinal tract involvement and in some cases with inflammatory bowel disease. Amyloidosis should be considered in atypical or treatment resistant, upper or lower chronic gastrointestinal symptoms. When associated with a familial history a lysozyme gene mutation must be searched.
doi:10.1186/1471-230X-14-159
PMCID: PMC4171570  PMID: 25217048
Amyloidosis; Lysozyme; Gastritis; Rectocolitis
3.  Lower vitamin D levels are associated with higher systemic lupus erythematosus activity, but not predictive of disease flare-up 
Lupus Science & Medicine  2014;1(1):e000027.
Objectives
Growing evidence suggests that vitamin D plays a key role in the pathogenesis and progression of autoimmune diseases, including systemic lupus erythematosus (SLE). Recent studies have found an association between lower serum 25-hydroxyvitamin D (25(OH)D) levels and higher SLE activity. We studied the relationship between 25(OH)D levels and Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score, and we assessed for the first time the role of vitamin D in predicting SLE flare-ups.
Methods
Serum 25(OH)D levels were measured in 170 patients with SLE who were prospectively followed up for 6 months (Plaquenil LUpus Systemic study, ClinicalTrials.gov number NCT00413361).
Results
The mean SLEDAI score was 2.03±2.43 and 12.3% patients had active disease (SLEDAI ≥6). The mean 25(OH)D level was 20.6±9.8 ng/mL. Deficiency (25(OH)D <10 ng/mL) was observed in 27 (15.9%), insufficiency (10≤25(OH)D<30) in 112 (65.9%) and optimal vitamin D status (25(OH)D≥30) in 31 (18.2%) patients. In multivariate analysis, female gender (p=0.018), absence of defined antiphospholipid syndrome (p=0.002) and higher creatinine clearance (p=0.004) were predictive of lower 25(OH)D levels. In multivariate analysis, lower 25(OH)D levels were associated with high SLE activity (p=0.02). Relapse-free survival rate was not statistically different according to the vitamin D status during the 6-month follow-up (p=0.22).
Conclusions
We found a low vitamin D status in the majority of patients with SLE, and a modest association between lower 25(OH)D levels and high disease activity. There was no association between baseline 25(OH)D levels and relapse-free survival rate.
doi:10.1136/lupus-2014-000027
PMCID: PMC4213833  PMID: 25379192
vitamin D; Systemic Lupus Erythematosus; Autoimmune Diseases; hydroxychloroquine
4.  Parenclitic networks: uncovering new functions in biological data 
Scientific Reports  2014;4:5112.
We introduce a novel method to represent time independent, scalar data sets as complex networks. We apply our method to investigate gene expression in the response to osmotic stress of Arabidopsis thaliana. In the proposed network representation, the most important genes for the plant response turn out to be the nodes with highest centrality in appropriately reconstructed networks. We also performed a target experiment, in which the predicted genes were artificially induced one by one, and the growth of the corresponding phenotypes compared to that of the wild-type. The joint application of the network reconstruction method and of the in vivo experiments allowed identifying 15 previously unknown key genes, and provided models of their mutual relationships. This novel representation extends the use of graph theory to data sets hitherto considered outside of the realm of its application, vastly simplifying the characterization of their underlying structure.
doi:10.1038/srep05112
PMCID: PMC4037713  PMID: 24870931
5.  Early-Onset Osteoarthritis, Charcot-Marie-Tooth Like Neuropathy, Autoimmune Features, Multiple Arterial Aneurysms and Dissections: An Unrecognized and Life Threatening Condition 
PLoS ONE  2014;9(5):e96387.
Background
Severe osteoarthritis and thoracic aortic aneurysms have recently been associated with mutations in the SMAD3 gene, but the full clinical spectrum is incompletely defined.
Methods
All SMAD3 gene mutation carriers coming to our centre and their families were investigated prospectively with a structured panel including standardized clinical workup, blood tests, total body computed tomography, joint X-rays. Electroneuromyography was performed in selected cases.
Results
Thirty-four SMAD3 gene mutation carriers coming to our centre were identified and 16 relatives were considered affected because of aortic surgery or sudden death (total 50 subjects). Aortic disease was present in 72%, complicated with aortic dissection, surgery or sudden death in 56% at a mean age of 45 years. Aneurysm or tortuosity of the neck arteries was present in 78%, other arteries were affected in 44%, including dissection of coronary artery. Overall, 95% of mutation carriers displayed either aortic or extra-aortic arterial disease. Acrocyanosis was also present in the majority of patients. Osteoarticular manifestations were recorded in all patients. Joint involvement could be severe requiring surgery in young patients, of unusual localization such as tarsus or shoulder, or mimicking crystalline arthropathy with fibrocartilage calcifications. Sixty eight percent of patients displayed neurological symptoms, and 9 suffered peripheral neuropathy. Electroneuromyography revealed an axonal motor and sensory neuropathy in 3 different families, very evocative of type II Charcot-Marie-Tooth (CMT2) disease, although none had mutations in the known CMT2 genes. Autoimmune features including Sjogren’s disease, rheumatoid arthritis, Hashimoto’s disease, or isolated autoantibodies- were found in 36% of patients.
Interpretation
SMAD3 gene mutations are associated with aortic dilatation and osteoarthritis, but also autoimmunity and peripheral neuropathy which mimics type II Charcot-Marie-Tooth.
doi:10.1371/journal.pone.0096387
PMCID: PMC4012990  PMID: 24804794
6.  Increased Arterial Stiffness in Systemic Lupus Erythematosus (SLE) Patients at Low Risk for Cardiovascular Disease: A Cross-Sectional Controlled Study 
PLoS ONE  2014;9(4):e94511.
Cardiovascular disease (CVD) is a major cause of death in systemic lupus erythematosus (SLE) patients. Although the risk for cardiovascular events in patients with SLE is significant, the absolute number of events per year in any given cohort remains small. Thus, CVD risks stratification in patients with SLE focuses on surrogate markers for atherosclerosis at an early stage, such as reduced elasticity of arteries. Our study was designed to determine whether arterial stiffness is increased in SLE patients at low risk for CVD and analyze the role for traditional and non-traditional CVD risk factors on arterial stiffness in SLE. Carotid-femoral pulse wave velocity (PWV) was prospectively assessed as a measure of arterial stiffness in 41 SLE patients and 35 controls (CTL). Adjustment on age or Framingham score was performed using a logistic regression model. Factors associated with PWV were identified separately in SLE patients and in controls using Pearson's correlation coefficient for univariate analysis and multiple linear regression for multivariate analysis. SLE patients and controls displayed a low 10-year risk for CVD according to Framingham score (1.8±3.6% in SLE vs 1.6±2.8% in CTL, p = 0.46). Pulse wave velocity was, however, higher in SLE patients (7.1±1.6 m/s) as compared to controls (6.3±0.8 m/s; p = 0.01, after Framingham score adjustment) and correlated with internal carotid wall thickness (p = 0.0017). In multivariable analysis, only systolic blood pressure (p = 0.0005) and cumulative dose of glucocorticoids (p = 0.01) were associated with PWV in SLE patients. Interestingly, the link between systolic blood pressure (SBP) and arterial stiffness was also confirmed in SLE patients with normal systolic blood pressure. In conclusion, arterial stiffness is increased in SLE patients despite a low risk for CVD according to Framingham score and is associated with systolic blood pressure and glucocorticoid therapy.
doi:10.1371/journal.pone.0094511
PMCID: PMC3983200  PMID: 24722263
7.  Measuring brain temperature without a thermometer 
doi:10.3389/fphys.2014.00124
PMCID: PMC3973909  PMID: 24723893
fluctuation-dissipation theorem; temperature; multi-thermalization; aging; weak ergodicity breaking; cognitive neuroscience; resting state
8.  Autoreactive IgE Is Prevalent in Systemic Lupus Erythematosus and Is Associated with Increased Disease Activity and Nephritis 
PLoS ONE  2014;9(2):e90424.
The presence of autoantibodies in systemic lupus erythematosus, particularly those of the IgG subclass, have long been associated with disease onset and activity. Here we explored the prevalence of autoreactive IgE in SLE and its relevance to disease in French (n = 79) and United States (US) (n = 117) cohorts with a mean age of 41.5±12.7 and 43.6±15.3 years and disease duration of 13.5±8.5 and 16.6±11.9 years, respectively. Our findings show that approximately 65% of all SLE subjects studied produced IgE antibodies to the seven autoantigens tested. This positivity was increased to almost 83% when only those subjects with active disease were considered. SLE subjects who were positive for anti-dsDNA, -Sm, and -SSB/La -specific IgE showed a highly significant association in the levels of these antibodies with disease activity similar to that of the corresponding IgG's. A strong association of IgE autoantibodies with active nephritis was also found in the combined cohort analysis. A test of the predictive value of autoreactive IgE’s and IgGs for disease activity (SLE Disease Activity Index (SLEDAI) ≥4) revealed that the best predictors were dsDNA-specific IgE and IgG, and that the age of an SLE subject influenced this predictive model. The finding argue that the overall levels of IgE autoantibodies, independently or in combination with IgG autoantibodies, may serve as indicators of active disease.
doi:10.1371/journal.pone.0090424
PMCID: PMC3938730  PMID: 24587356
9.  Emergence of Small-World Anatomical Networks in Self-Organizing Clustered Neuronal Cultures 
PLoS ONE  2014;9(1):e85828.
In vitro primary cultures of dissociated invertebrate neurons from locust ganglia are used to experimentally investigate the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. At all the different stages of the culture's development, identification of neurons' and neurites' location by means of a dedicated software allows to ultimately extract an adjacency matrix from each image of the culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main network's characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graph's micro- and meso-scale properties emerge. Finally, we identify the main physical processes ruling the culture's morphological transformations, and embed them into a simplified growth model qualitatively reproducing the overall set of experimental observations.
doi:10.1371/journal.pone.0085828
PMCID: PMC3904852  PMID: 24489675
10.  Rheology Measurements for Online Monitoring of Solids in Activated Sludge Reactors of Municipal Wastewater Treatment Plant 
The Scientific World Journal  2014;2014:590961.
Rheological behaviour of recycled sludge from a secondary clarifier of a municipal wastewater treatment plant was studied by using the rate controlled coaxial cylinder viscometer Rotovisko-Haake 20, system M5-osc., measuring device NV. The tests (hysteresis cycles) were performed under continuous flow conditions and following an ad hoc measurement protocol. Sludge shear stress versus shear rate curves were fitted very satisfactorily by rheological models. An experimental equation correlating the solid concentration of sludge to relative viscosity and fitting satisfactorily flow curves at different Total Suspended Solids (TTS%) was obtained. Application of the empirical correlation should allow the monitoring of the proper functioning of a wastewater treatment plant measuring viscosity of sludge.
doi:10.1155/2014/590961
PMCID: PMC3914390  PMID: 24550715
11.  Reconstructing functional brain networks: have we got the basics right? 
doi:10.3389/fnhum.2014.00107
PMCID: PMC3936558  PMID: 24578687
complex networks theory; functional brain networks; correlations; synchronization; data mining
12.  Functional significance of complex fluctuations in brain activity: from resting state to cognitive neuroscience 
Behavioral studies have shown that human cognition is characterized by properties such as temporal scale invariance, heavy-tailed non-Gaussian distributions, and long-range correlations at long time scales, suggesting models of how (non observable) components of cognition interact. On the other hand, results from functional neuroimaging studies show that complex scaling and intermittency may be generic spatio-temporal properties of the brain at rest. Somehow surprisingly, though, hardly ever have the neural correlates of cognition been studied at time scales comparable to those at which cognition shows scaling properties. Here, we analyze the meanings of scaling properties and the significance of their task-related modulations for cognitive neuroscience. It is proposed that cognitive processes can be framed in terms of complex generic properties of brain activity at rest and, ultimately, of functional equations, limiting distributions, symmetries, and possibly universality classes characterizing them.
doi:10.3389/fnsys.2014.00112
PMCID: PMC4052734  PMID: 24966818
scaling; multifractals; ageing; weak ergodicity breaking; symmetry; fluctuation-dissipation theorem; cognitive neuroscience; resting state
13.  Time scales in cognitive neuroscience 
Cognitive neuroscience boils down to describing the ways in which cognitive function results from brain activity. In turn, brain activity shows complex fluctuations, with structure at many spatio-temporal scales. Exactly how cognitive function inherits the physical dimensions of neural activity, though, is highly non-trivial, and so are generally the corresponding dimensions of cognitive phenomena. As for any physical phenomenon, when studying cognitive function, the first conceptual step should be that of establishing its dimensions. Here, we provide a systematic presentation of the temporal aspects of task-related brain activity, from the smallest scale of the brain imaging technique's resolution, to the observation time of a given experiment, through the characteristic time scales of the process under study. We first review some standard assumptions on the temporal scales of cognitive function. In spite of their general use, these assumptions hold true to a high degree of approximation for many cognitive (viz. fast perceptual) processes, but have their limitations for other ones (e.g., thinking or reasoning). We define in a rigorous way the temporal quantifiers of cognition at all scales, and illustrate how they qualitatively vary as a function of the properties of the cognitive process under study. We propose that each phenomenon should be approached with its own set of theoretical, methodological and analytical tools. In particular, we show that when treating cognitive processes such as thinking or reasoning, complex properties of ongoing brain activity, which can be drastically simplified when considering fast (e.g., perceptual) processes, start playing a major role, and not only characterize the temporal properties of task-related brain activity, but also determine the conditions for proper observation of the phenomena. Finally, some implications on the design of experiments, data analyses, and the choice of recording parameters are discussed.
doi:10.3389/fphys.2013.00086
PMCID: PMC3630296  PMID: 23626578
cognitive neuroscience; characteristic time; relaxation time; observation time; non-Gaussianity; scaling; fluctuation-dissipation theorem; non-self-averaging
14.  Knowledge Discovery in Spectral Data by Means of Complex Networks 
Metabolites  2013;3(1):155-167.
In the last decade, complex networks have widely been applied to the study of many natural and man-made systems, and to the extraction of meaningful information from the interaction structures created by genes and proteins. Nevertheless, less attention has been devoted to metabonomics, due to the lack of a natural network representation of spectral data. Here we define a technique for reconstructing networks from spectral data sets, where nodes represent spectral bins, and pairs of them are connected when their intensities follow a pattern associated with a disease. The structural analysis of the resulting network can then be used to feed standard data-mining algorithms, for instance for the classification of new (unlabeled) subjects. Furthermore, we show how the structure of the network is resilient to the presence of external additive noise, and how it can be used to extract relevant knowledge about the development of the disease.
doi:10.3390/metabo3010155
PMCID: PMC3901251  PMID: 24957895
complex networks; data mining; spectroscopy; classification
15.  Emergence of network features from multiplexity 
Scientific Reports  2013;3:1344.
Many biological and man-made networked systems are characterized by the simultaneous presence of different sub-networks organized in separate layers, with links and nodes of qualitatively different types. While during the past few years theoretical studies have examined a variety of structural features of complex networks, the outstanding question is whether such features are characterizing all single layers, or rather emerge as a result of coarse-graining, i.e. when going from the multilayered to the aggregate network representation. Here we address this issue with the help of real data. We analyze the structural properties of an intrinsically multilayered real network, the European Air Transportation Multiplex Network in which each commercial airline defines a network layer. We examine how several structural measures evolve as layers are progressively merged together. In particular, we discuss how the topology of each layer affects the emergence of structural properties in the aggregate network.
doi:10.1038/srep01344
PMCID: PMC3583169  PMID: 23446838
16.  Expression of 8-OHdG in Zosterisessor ophiocephalus from the Venetian lagoon, Italy 
The aim of the present work was to evaluate the expression of 8-OHdG (8-hydroxy-2'-deoxyguanosine) in the benthic fish Zosterisessor ophiocephalus collected in two differently polluted sites of the Venetian lagoon (Porto Marghera and Caroman). We compared our data on 8-OHdG with those of CYP1A (Cytochrome P450, family 1, subfamily A, polypeptide 1), which is a well known biomarker for detoxification of contaminants. Immunohistochemistry with an antibody to 8-OHdG showed immunopositivity in nuclei of hepatocytes as well as in melanomacrophage centres of spleen and kidney, whereas an anti-CYP1A antibody exhibited positive immunostaining in the liver, kidney and ovary. The liver of males showed higher expression of both proteins than females. In animals from Porto Marghera site, the enzymatic assay for 8-OHdG exhibited higher levels in liver of males than in females. Western Blot analysis using the antibody anti-CYP1A recognized the presence of a band of about 60 kDa in the liver of males and females. Males exhibited a strong band, whereas in females the band showed a lower intensity. By using Real-Time PCR, the mRNA expression of CYP1A did not show any differences between males and females from each site, but it was at borderline significance level. Comparing the two sites, mRNA expression of CYP1A was significantly higher in the liver of both males and females from Porto Marghera than that of Caroman. The present data suggest that pollutants are bio-available as demonstrated by our biomarker analyses and may have a harmful effect on aquatic organisms such as Z. ophiocephalus. We report that the highest levels of hepatic 8-OHdG and CYP1A expression were detected in males, showing clear gender specificity.
doi:10.4081/ejh.2013.e8
PMCID: PMC3683615  PMID: 23549467
OHdG; CYP1A; fish; immunohistochemistry; molecular biology.
17.  Explosive transitions to synchronization in networks of phase oscillators 
Scientific Reports  2013;3:1281.
The emergence of dynamical abrupt transitions in the macroscopic state of a system is currently a subject of the utmost interest. The occurrence of a first-order phase transition to synchronization of an ensemble of networked phase oscillators was reported, so far, for very particular network architectures. Here, we show how a sharp, discontinuous transition can occur, instead, as a generic feature of networks of phase oscillators. Precisely, we set conditions for the transition from unsynchronized to synchronized states to be first-order, and demonstrate how these conditions can be attained in a very wide spectrum of situations. We then show how the occurrence of such transitions is always accompanied by the spontaneous setting of frequency-degree correlation features. Third, we show that the conditions for abrupt transitions can be even softened in several cases. Finally, we discuss, as a possible application, the use of this phenomenon to express magnetic-like states of synchronization.
doi:10.1038/srep01281
PMCID: PMC3573336  PMID: 23412391
18.  Losartan reduces trinitrobenzene sulphonic acid-induced colorectal fibrosis in rats 
Intestinal fibrosis – a chronic and progressive process mediated by several factors – occurs in several fibrostenosing enteropathies, but most frequently in patients with Crohn’s disease (CD). Despite the advances made in the understanding of CD and its management over the past 20 years, surgical intervention remains the only treatment strategy for patients with fibrostenosing CD. The results of several studies, however, have suggested that fibrosis may be a reversible and/or preventable phenomenon. Following an overview summarizing the contemporary knowledge regarding the cellular, cytokine and growth factor interactions that contribute to inflammation and the progression of fibrosis, this article describes an experimental animal model of colitis resembling human CD, which the authors used to investigate whether losartan, an angiotensin II receptor antagonist, could be used as a prophylactic agent to reduce the risk of intestinal fibrosis and strictures in patients with CD.
BACKGROUND:
Intestinal fibrosis is a challenging clinical condition in several fibrostenosing enteropathies, particularly Crohn’s disease. Currently, no effective preventive measures or medical therapies are available for intestinal fibrosis. Fibrosis, due to an abnormal accumulation of extracellular matrix proteins, is a chronic and progressive process mediated by cell/matrix/cytokine and growth factor interactions, but may be a reversible phenomenon. Of the several molecules regulating fibrogenesis, transforming growth factor-beta 1 (TGF-β1) appears to play a pivotal role; it is strongly induced by the local activation of angiotensin II. The levels of both TGF-β1 and angiotensin II are elevated in fibrostenosing Crohn’s disease.
AIMS:
To evaluate the in vivo effect of losartan – an angiotensin II receptor antagonist – on the course of chronic colitis-associated fibrosis and on TGF-β1 expression.
METHODS:
Colitis was induced by intrarectal instillation of trinitrobenzene sulphonic acid (TNBS) (15 mg/mL) while losartan was administered orally daily by gavage (7 mg/kg/day) for 21 days. Three groups of rats were evaluated: control (n=10); TNBS treated (n=10); and TNBS + losartan treated (n=10). Inflammation and fibrosis of the colon were evaluated by macro- and microscopic score analysis. Colonic TGF-β1 levels was measured using ELISA.
RESULTS:
Twenty-one days after induction, losartan significantly improved the macro- and microscopic scores of fibrosis in the colonic wall and reduced TGF-β1 concentration.
CONCLUSIONS:
Prophylactic oral administration of losartan reduces the colorectal fibrosis complicating the TNBS-induced chronic colitis, an effect that appears to be mediated by a downregulation of TGF-β1 expression.
PMCID: PMC3275403  PMID: 22288068
Angiotensin II receptor antagonist; Experimental colitis; Fibrosis; Inflammatory bowel disease; Losartan; TGF-β1; TNBS
19.  Why should cognitive neuroscientists study the brain's resting state? 
doi:10.3389/fnhum.2013.00045
PMCID: PMC3576622  PMID: 23431277
20.  Efficient neural codes can lead to spurious synchronization 
doi:10.3389/fncom.2013.00125
PMCID: PMC3767907  PMID: 24058342
synchronization; neural models; boolean code; EEG/MEG; stimuli
21.  Optimizing Functional Network Representation of Multivariate Time Series 
Scientific Reports  2012;2:630.
By combining complex network theory and data mining techniques, we provide objective criteria for optimization of the functional network representation of generic multivariate time series. In particular, we propose a method for the principled selection of the threshold value for functional network reconstruction from raw data, and for proper identification of the network's indicators that unveil the most discriminative information on the system for classification purposes. We illustrate our method by analysing networks of functional brain activity of healthy subjects, and patients suffering from Mild Cognitive Impairment, an intermediate stage between the expected cognitive decline of normal aging and the more pronounced decline of dementia. We discuss extensions of the scope of the proposed methodology to network engineering purposes, and to other data mining tasks.
doi:10.1038/srep00630
PMCID: PMC3433690  PMID: 22953051
22.  Targeting the dynamics of complex networks 
Scientific Reports  2012;2:396.
We report on a generic procedure to steer (target) a network's dynamics towards a given, desired evolution. The problem is here tackled through a Master Stability Function approach, assessing the stability of the aimed dynamics, and through a selection of nodes to be targeted. We show that the degree of a node is a crucial element in this selection process, and that the targeting mechanism is most effective in heterogeneous scale-free architectures. This makes the proposed approach applicable to the large majority of natural and man-made networked systems.
doi:10.1038/srep00396
PMCID: PMC3343324  PMID: 22563525

Results 1-25 (48)