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Optimal network topologies: Expanders, Cages, Ramanujan graphs, Entangled networks and all that
Luca Donetti,Franco Neri,Miguel A. Munoz
Physics , 2006, DOI: 10.1088/1742-5468/2006/08/P08007
Abstract: We report on some recent developments in the search for optimal network topologies. First we review some basic concepts on spectral graph theory, including adjacency and Laplacian matrices, and paying special attention to the topological implications of having large spectral gaps. We also introduce related concepts as ``expanders'', Ramanujan, and Cage graphs. Afterwards, we discuss two different dynamical feautures of networks: synchronizability and flow of random walkers and so that they are optimized if the corresponding Laplacian matrix have a large spectral gap. From this, we show, by developing a numerical optimization algorithm that maximum synchronizability and fast random walk spreading are obtained for a particular type of extremely homogeneous regular networks, with long loops and poor modular structure, that we call entangled networks. These turn out to be related to Ramanujan and Cage graphs. We argue also that these graphs are very good finite-size approximations to Bethe lattices, and provide almost or almost optimal solutions to many other problems as, for instance, searchability in the presence of congestion or performance of neural networks. Finally, we study how these results are modified when studying dynamical processes controlled by a normalized (weighted and directed) dynamics; much more heterogeneous graphs are optimal in this case. Finally, a critical discussion of the limitations and possible extensions of this work is presented.
Infertility in Men with Varicocele: The Role of Age, Smoking and Alcohol Intake  [PDF]
Luca Coppeta, Anna Neri, Maria Nicotra, Vincenzo Gentile, Claudio Spina, Adalgisa Pietropolli, Fulvia Gloria-Bottini
Health (Health) , 2020, DOI: 10.4236/health.2020.123019
Abstract: Previous studies have focused on the damaging effects of smoking and alcohol on sperm parameters; however, some of these studies have failed to find a significant correlation between these variables. Herein we have investigated the relationship of infertility with smoking and/or alcohol consumption in one hundred and thirty-six men with varicocele, admitted consecutively to the Outpatients Department of Infertility at the University of Rome La Sapienza (Italy) between 2005-2007. The sample size was small because we have selected couples with both marital infertility lasting for more than two years and the male partner with varicocele. Statistical analyses were carried out using the software of Statistical Package for the Social Sciences (SPSS). We showed a highly significant association of infertility with alcohol consumption. As the mean value was 32 years, comparing men of age less than or equal to 32 years and men of age over 32 years, this association is present only in men of age less than or equal to 32 years. A discriminant analysis with infertility as dependent variable and age, alcohol consumption and smoking habit as independent variables has shown a significant discrimination only in men of age less than or equal to 32 years. The most important contribution to this discrimination was given by alcohol followed by age while contribution from smoking was small. Our analyses suggest that alcohol consumption contributes to infertility in men of age less than or equal to 32 years whereas smoking does not.
Characterizing the relationship between health utility and renal function after kidney transplantation in UK and US: a cross-sectional study
Neri Luca,McEwan Phil,Sennf？lt Karin,Baboolal Kesh
Health and Quality of Life Outcomes , 2012, DOI: 10.1186/1477-7525-10-139
Abstract: Background Chronic allograft nephropathy (CAN) occurs in a large share of transplant recipients and it is the leading cause of graft loss despite the introduction of new and effective immunosuppressants. The reduction in renal function secondary to immunologic and non-immunologic CAN leads to several complications, including anemia and calcium-phosphorus metabolism imbalance and may be associated to worsening Health-Related Quality of Life. We sought to evaluate the relationship between kidney function and Euro-Qol 5 Dimension Index (EQ-5Dindex) scores after kidney transplantation and evaluate whether cross-cultural differences exist between UK and US. Methods This study is a secondary analysis of existing data gathered from two cross-sectional studies. We enrolled 233 and 209 subjects aged 18–74 years who received a kidney transplant in US and UK respectively. For the present analysis we excluded recipients with multiple or multi-organ transplantation, creatinine kinase ≥200 U/L, acute renal failure, and without creatinine assessments in 3 months pre-enrollment leaving 281 subjects overall. The questionnaires were administered independently in the two centers. Both packets included the EQ-5Dindex and socio-demographic items. We augmented the analytical dataset with information abstracted from clinical charts and administrative records including selected comorbidities and biochemistry test results. We used ordinary least squares and quantile regression adjusted for socio-demographic and clinical characteristics to assess the association between EQ-5Dindex and severity of chronic kidney disease (CKD). Results CKD severity was negatively associated with EQ-5Dindex in both samples (UK: ρ= 0.20, p=0.02; US: ρ= 0.21, p=0.02). The mean adjusted disutility associated to CKD stage 5 compared to CKD stage 1–2 was Δ= 0.38 in the UK sample, Δ= 0.11 in the US sample and Δ= 0.22 in the whole sample. The adjusted median disutility associated to CKD stage 5 compared to CKD stage 1–2 for the whole sample was 0.18 (p<0.01, quantile regression). Center effect was not statistically significant. Conclusions Impaired renal function is associated with reduced health-related quality of life independent of possible confounders, center-effect and analytic framework.
Seismic response to stress-strain fields in the lithosphere of Sicily
G. Barberi,D. Caccamo,G. De Luca,G. Neri
Annals of Geophysics , 1999, DOI: 10.4401/ag-3760
Abstract: Earthquake locations and fault-plane solutions are investigated in Sicily and the surrounding areas, by using local network data for the period 1988-1995, and a recently proposed 3D model of the local crustal structure. The results were used for local-to-regional scale stress inversion and strain tensor computations, after integration by a set of selected focal mechanisms taken from the literature. The area under study appears to be affected by heterogeneity of seismic deformation and the stress field. The contraction-to-extension transition from west to east on a regional scale can find a reasonable explanation in the framework of current geodynamic models, such as those assuming the activity of two main tectonic sources in the South Italy region, e.g., the Africa-Europe north-south slow convergence and the faster eastward roll-back of a westward-dipping Ionian subducting slab (Cinque al., 1993). The analysis of low-magnitude (2.5-4.0) earthquakes permitted us to perform an investigation of local-scale strain heterogeneities in this region and to evidence notable changes in the deformation style when processes at different scales are considered.
Wireless Sensing Based on RFID and Capacitive Technologies for Safety in Marble Industry Process Control
Fabrizio Iacopetti,Sergio Saponara,Luca Fanucci,Bruno Neri
Journal of Computer Networks and Communications , 2013, DOI: 10.1155/2013/392056
Abstract:
Wireless Sensing Based on RFID and Capacitive Technologies for Safety in Marble Industry Process Control
Fabrizio Iacopetti,Sergio Saponara,Luca Fanucci,Bruno Neri
Journal of Computer Networks and Communications , 2013, DOI: 10.1155/2013/392056
Abstract: This paper presents wireless sensing systems to increase safety and robustness in industrial process control, particularly in industrial machines for marble slab working. The process is performed by abrasive or cutting heads activated independently by the machine controller when the slab, transported on a conveyer belt, is under them. Current slab detection systems are based on electromechanical or optical devices at the machine entrance stage, suffering from deterioration and from the harsh environment. Slab displacement or break inside the machine due to the working stress may result in safety issues and damages to the conveyer belt due to incorrect driving of the working tools. The experimented contactless sensing techniques are based on four RFID and two capacitive sensing technologies and on customized hardware/software. The proposed solutions aim at overcoming some limitations of current state-of-the-art detection systems, allowing for reliable slab detection, outside and/or inside the machine, while maintaining low complexity and at the same time robustness to industrial harsh conditions. The proposed sensing devices may implement a wireless or wired sensor network feeding detection data to the machine controller. Data integrity check and process control algorithms have to be implemented for the safety and reliability of the overall industrial process. 1. Introduction The transformation of stone blocks coming from quarries into finished products, for example, tiles, sculptures, building materials, stone powder, and so forth, is performed through several different industrial processes. In the case of slab-shaped products (e.g., tiles), marble blocks coming from quarries are firstly sawn by a gangsaw [1] into marble slabs with a resulting irregular contour and with rough surfaces. Slabs are afterwards polished in a polishing machine [2], cut into smaller and regular slabs by means of cutting machines, and finally become end products. The process control of marble slab working is nowadays mainly based on a feed-forward control scheme: the marble slab is transported inside the machine by a conveyer belt; at the entrance of the machine, contact or optical sensing technologies are used to derive information on the presence and shape of the slab which are then used by the machine controlling system to drive the working heads on the slab when it is passing under them. Due to unforeseen events that may occur to the slab inside the machine, mainly slab displacement and cracks, the controlling system may drive the working heads on the base of not up-to-date
Sub kBT micro electromechanical irreversible logic gate
Miquel Lopez-Suarez,Igor Neri,Luca Gammaitoni
Mathematics , 2015,
Abstract: In modern computers, computation is performed by assembling together sets of logic gates. Popular gates like AND, OR, XOR, processing two logic inputs and yielding one logic output, are often addressed as irreversible logic gates; a sole knowledge of the output logic value, is not sufficient to infer the logic value of the two inputs. This lack of linkage between logical and physical irreversibility has animated a long debate [1,2] and been, recently, clarified[3] from a purely theoretical point of view; however, it is still missing experimental verification. In the following we present an experiment wherein we show that a combinational device that implements the OR gate logic, realized with a micro electromechanical cantilever, can be operated with energy as low as 0.05 kB T (with kB the Boltzman constant and T the room temperature), provided the operation is slow enough and frictional phenomena are properly addressed.
An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma
Domenica Ronchetti, Marta Lionetti, Laura Mosca, Luca Agnelli, Adrian Andronache, Sonia Fabris, Giorgio Deliliers, Antonino Neri
BMC Medical Genomics , 2008, DOI: 10.1186/1755-8794-1-37
Abstract: miRNA expression was quantified by Quantitative Real-Time PCR. Gene expression and genome profiling data were generated on Affymetrix oligonucleotide microarrays. Significant Analysis of Microarrays algorithm was used to investigate differentially expressed transcripts. Conventional statistics were used to test correlations for significance. Public libraries were queried to predict putative miRNA targets.We identified transcripts specific to six miRNA host genes (CCPG1, GULP1, EVL, TACSTD1, MEST, and TNIK) whose average changes in expression varied at least 2-fold from the mean of the examined dataset. We evaluated the expression levels of the corresponding intronic miRNAs and identified a significant correlation between the expression levels of MEST, EVL, and GULP1 and those of the corresponding miRNAs miR-335, miR-342-3p, and miR-561, respectively. Genome-wide profiling of the 20 HMCLs indicated that the increased expression of the three host genes and their corresponding intronic miRNAs was not correlated with local copy number variations. Notably, miRNAs and their host genes were overexpressed in a fraction of primary tumors with respect to normal plasma cells; however, this finding was not correlated with known molecular myeloma groups. The predicted putative miRNA targets and the transcriptional profiles associated with the primary tumors suggest that MEST/miR-335 and EVL/miR-342-3p may play a role in plasma cell homing and/or interactions with the bone marrow microenvironment.Our data support the idea that intronic miRNAs and their host genes are regulated dependently, and may contribute to the understanding of their biological roles in cancer. To our knowledge, this is the first evidence of deregulated miRNA expression in MM, providing insights that may lead to the identification of new biomarkers and altered molecular pathways of the disease.Multiple myeloma (MM) is a plasma cell neoplasia characterized by profound genomic instability involving numerical an
Human Adipose Stromal Cells (ASC) for the Regeneration of Injured Cartilage Display Genetic Stability after In Vitro Culture Expansion
Simona Neri, Philippe Bourin, Julie-Anne Peyrafitte, Luca Cattini, Andrea Facchini, Erminia Mariani
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0077895
Abstract: Mesenchymal stromal cells are emerging as an extremely promising therapeutic agent for tissue regeneration due to their multi-potency, immune-modulation and secretome activities, but safety remains one of the main concerns, particularly when in vitro manipulation, such as cell expansion, is performed before clinical application. Indeed, it is well documented that in vitro expansion reduces replicative potential and some multi-potency and promotes cell senescence. Furthermore, during in vitro aging there is a decrease in DNA synthesis and repair efficiency thus leading to DNA damage accumulation and possibly inducing genomic instability. The European Research Project ADIPOA aims at validating an innovative cell-based therapy where autologous adipose stromal cells (ASCs) are injected in the diseased articulation to activate regeneration of the cartilage. The primary objective of this paper was to assess the safety of cultured ASCs. The maintenance of genetic integrity was evaluated during in vitro culture by karyotype and microsatellite instability analysis. In addition, RT-PCR array-based evaluation of the expression of genes related to DNA damage signaling pathways was performed. Finally, the senescence and replicative potential of cultured cells was evaluated by telomere length and telomerase activity assessment, whereas anchorage-independent clone development was tested in vitro by soft agar growth. We found that cultured ASCs do not show genetic alterations and replicative senescence during the period of observation, nor anchorage-independent growth, supporting an argument for the safety of ASCs for clinical use.
Motor proteins traffic regulation by supply-demand balance of resources
Luca Ciandrini,I. Neri,Jean-Charles Walter,O. Dauloudet,A. Parmeggiani
Quantitative Biology , 2014, DOI: 10.1088/1478-3975/11/5/056006
Abstract: In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work we provide a theoretical framework to study, analytically and numerically, how motor density profiles and crowding along cytoskeletal filaments depend on the competition of motors for their binding sites. We propose two models in which finite processive motor proteins actively advance along cytoskeletal filaments and are continuously exchanged with the motor pool. We first look at homogeneous reservoirs and then examine the effects of free motor diffusion in the surrounding medium. We consider as a reference situation recent in vitro experimental setups of kinesin-8 motors binding and moving along microtubule filaments in a flow chamber. We investigate how the crowding of linear motor proteins moving on a filament can be regulated by the balance between supply (concentration of motor proteins in the flow chamber) and demand (total number of polymerised tubulin heterodimers). We present analytical results for the density profiles of bound motors, the reservoir depletion, and propose novel phase diagrams that present the formation of jams of motor proteins on the filament as a function of two tuneable experimental parameters: the motor protein concentration and the concentration of tubulins polymerized into cytoskeletal filaments. Extensive numerical simulations corroborate the analytical results for parameters in the experimental range and also address the effects of diffusion of motor proteins in the reservoir.
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