Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically infeasible, even in simpler systems like dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct structural connectivity from network activity monitored through calcium imaging. We focus in this study on the inference of excitatory synaptic links. Based on information theory, our method requires no prior assumptions on the statistics of neuronal firing and neuronal connections. The performance of our algorithm is benchmarked on surrogate time series of calcium fluorescence generated by the simulated dynamics of a network with known ground-truth topology. We find that the functional network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (bursting or non-bursting). Thus by conditioning with respect to the global mean activity, we improve the performance of our method. This allows us to focus the analysis to specific dynamical regimes of the network in which the inferred functional connectivity is shaped by monosynaptic excitatory connections, rather than by collective synchrony. Our method can discriminate between actual causal influences between neurons and spurious non-causal correlations due to light scattering artifacts, which inherently affect the quality of fluorescence imaging. Compared to other reconstruction strategies such as cross-correlation or Granger Causality methods, our method based on improved Transfer Entropy is remarkably more accurate. In particular, it provides a good estimation of the excitatory network clustering coefficient, allowing for discrimination between weakly and strongly clustered topologies. Finally, we demonstrate the applicability of our method to analyses of real recordings of in vitro disinhibited cortical cultures where we suggest that excitatory connections are characterized by an elevated level of clustering compared to a random graph (although not extreme) and can be markedly non-local.

Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

Identification of neuronal network properties from the spectral analysis of calcium imaging signals in neuronal cultures

Neuronal networks in vitro are prominent systems to study the development of connections in living neuronal networks and the interplay between connectivity, activity and function. These cultured networks show a rich spontaneous activity that evolves concurrently with the connectivity of the underlying network. In this work we monitor the development of neuronal cultures, and record their activity using calcium fluorescence imaging. We use spectral analysis to characterize global dynamical and structural traits of the neuronal cultures. We first observe that the power spectrum can be used as a signature of the state of the network, for instance when inhibition is active or silent, as well as a measure of the network's connectivity strength. Second, the power spectrum identifies prominent developmental changes in the network such as GABAA switch. And third, the analysis of the spatial distribution of the spectral density, in experiments with a controlled disintegration of the network through CNQX, an AMPA-glutamate receptor antagonist in excitatory neurons, reveals the existence of communities of strongly connected, highly active neurons that display synchronous oscillations. Our work illustrates the interest of spectral analysis for the study of in vitro networks, and its potential use as a network-state indicator, for instance to compare healthy and diseased neuronal networks.

Use of social networks for academic purposes: a case study

Purpose This paper aims to analyse various aspects of an academic social network: the profile of users, the reasons for its use, its perceived benefits and the use of other social media for scholarly purposes. Design/methodology/approach The authors examined the profiles of the users of an academic social network. The users were affiliated with 12 universities. The following were recorded for each user: sex, the number of documents uploaded, the number of followers, and the number of people being followed. In addition, a survey was sent to the individuals who had an email address in their profile. Findings Half of the users of the social network were academics and a third were PhD students. Social sciences scholars accounted for nearly half of all users. Academics used the service to get in touch with other scholars, disseminate research results and follow other scholars. Other widely employed social media included citation indexes, document creation, edition and sharing tools and communication tools. Users complained about the lack of support for the utilisation of these tools. Research limitations/implications The results are based on a single case study. Originality/value This study provides new insights on the impact of social media in academic contexts by analysing the user profiles and benefits of a social network service that is specifically targeted at the academic community.

Exploring the use of mobile communications in a retirement home in Toronto: Preliminary results

This paper describes preliminary results of a qualitative case study on mobile communication conducted in an elders¿ retirement home in Toronto (Ontario, Canada) in May 2012. This is part of an international research project on the relationship between mobile communications and older people.Secondary data at a Canadian level contextualizes the case study. We focus ondemographic characteristics and on adoption and use of information and communication technologies (ICTs) broken by age.Participants in the study (21 individuals) are between 75 and 98 years of age, thereforewe can consider that the gathered evidence refers to the ¿old¿ older. Mobile phoneusers in the sample describe very specific uses of the mobile phone, while non-usersreport not facing external pressures for adopting that technology. The main channel formediated communication is the landline; in consequences mobile phones ¿when used¿ constitute an extra layer of communication. Finally, when members of the personal network of the individuals live abroad they are more prone to use Internet and Skype. We are also able to find ex-users of both mobile telephony and computers/internet who stopped using these technologies because they did not find any use for them.

Energy-based modelling and simulation of the interconnection of a back-to-back converter and a doubly-fed induction machine

This paper describes the port interconnection of two subsystems: a power electronics subsystem (a back-to-back AC/CA converter (B2B), coupled to a phase of the power grid), and an electromechanical subsystem (a doubly-fed induction machine (DFIM). The B2B is a variable structure system (VSS), due to presence of control-actuated switches: however, from a modelling simulation, as well as a control-design, point of view, it is sensible to consider modulated transformers (MTF in the bond graph language) instead of the pairs of complementary switches. The port-Hamiltonian models of both subsystems are presented and, using a power-preserving interconnection, the Hamiltonian description of the whole system is obtained; detailed bond graphs of all subsystems and the complete system are also provided. Using passivity-based controllers computed in the Hamiltonian formalism for both subsystems, the whole model is simulated; simulations are run to rest the correctness and efficiency of the Hamiltonian network modelling approach used in this work.

Natural or naturalized? phylogeography suggests that the abundant sea urchin arbacia lixula Is a recent Colonizer of the Mediterranean

We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94-205 kya in the Mediterranean, and 31-67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.

Tobacco control policies in hospitals before and after the implementation of a national smoking ban in Catalonia, Spain

Background: Diverse projects and guidelines to assist hospitals towards the attainment of comprehensive smoke-free policies have been developed. In 2006, Spain government passed a new smoking ban that reinforce tobacco control policies and banned completely smoking in hospitals. This study assesses the progression of tobacco control policies in the Catalan Network of Smokefree Hospitals before and after a comprehensive national smoking ban. Methods: We used the Self-Audit Questionnaire of the European Network for Smoke-free Hospitals to score the compliance of 9 policy standards (global score = 102). We used two crosssectional surveys to evaluate tobacco control policies before (2005) and after the implementation of a national smoking ban (2007) in 32 hospitals of Catalonia, Spain. We compared the means of the overall score in 2005 and 2007 according to the type of hospital, the number of beds, the prevalence of tobacco consumption, and the number of years as a smoke-free hospital. Results: The mean of the implementation score of tobacco control policies was 52.4 (95% CI:45.4-59.5) in 2005 and 71.6 (95% CI: 67.0-76.2) in 2007 with an increase of 36.7% (p < 0.01). The hospitals with greater improvement were general hospitals (48% increase; p < 0.01), hospitals with > 300 beds (41.1% increase; p < 0.01), hospitals with employees' tobacco consumption prevalence 35-39% (72.2% increase; p < 0.05) and hospitals that had recently implemented smoke-free policies (74.2% increase; p < 0.01). Conclusion: The national smoking ban appears to increase tobacco control activities in hospitals combined with other non-bylaw initiatives such as the Smoke-free Hospital Network.

Tobacco control policies in hospitals before and after the implementation of a national smoking ban in Catalonia, Spain

Background: Diverse projects and guidelines to assist hospitals towards the attainment of comprehensive smoke-free policies have been developed. In 2006, Spain government passed a new smoking ban that reinforce tobacco control policies and banned completely smoking in hospitals. This study assesses the progression of tobacco control policies in the Catalan Network of Smokefree Hospitals before and after a comprehensive national smoking ban. Methods: We used the Self-Audit Questionnaire of the European Network for Smoke-free Hospitals to score the compliance of 9 policy standards (global score = 102). We used two crosssectional surveys to evaluate tobacco control policies before (2005) and after the implementation of a national smoking ban (2007) in 32 hospitals of Catalonia, Spain. We compared the means of the overall score in 2005 and 2007 according to the type of hospital, the number of beds, the prevalence of tobacco consumption, and the number of years as a smoke-free hospital. Results: The mean of the implementation score of tobacco control policies was 52.4 (95% CI:45.4-59.5) in 2005 and 71.6 (95% CI: 67.0-76.2) in 2007 with an increase of 36.7% (p < 0.01). The hospitals with greater improvement were general hospitals (48% increase; p < 0.01), hospitals with > 300 beds (41.1% increase; p < 0.01), hospitals with employees' tobacco consumption prevalence 35-39% (72.2% increase; p < 0.05) and hospitals that had recently implemented smoke-free policies (74.2% increase; p < 0.01). Conclusion: The national smoking ban appears to increase tobacco control activities in hospitals combined with other non-bylaw initiatives such as the Smoke-free Hospital Network.

Use of social networks for academic purposes: a case study

Purpose- This paper aims to analyse various aspects of an academic social network: the profile of users, the reasons for its use, its perceived benefits and the use of other social media for scholarly purposes. Design/methodology/approach- The authors examined the profiles of the users of an academic social network. The users were affiliated with 12 universities. The following were recorded for each user: sex, the number of documents uploaded, the number of followers, and the number of people being followed. In addition, a survey was sent to the individuals who had an email address in their profile. Findings- Half of the users of the social network were academics and a third were PhD students. Social sciences scholars accounted for nearly half of all users. Academics used the service to get in touch with other scholars, disseminate research results and follow other scholars. Other widely employed social media included citation indexes, document creation, edition and sharing tools and communication tools. Users complained about the lack of support for the utilisation of these tools. Research limitations/implications- The results are based on a single case study. Originality/value- This study provides new insights on the impact of social media in academic contexts by analysing the user profiles and benefits of a social network service that is specifically targeted at the academic community.

Identification of neuronal network properties from the spectral analysis of calcium imaging signals in neuronal cultures

Neuronal networks in vitro are prominent systems to study the development of connections in living neuronal networks and the interplay between connectivity, activity and function. These cultured networks show a rich spontaneous activity that evolves concurrently with the connectivity of the underlying network. In this work we monitor the development of neuronal cultures, and record their activity using calcium fluorescence imaging. We use spectral analysis to characterize global dynamical and structural traits of the neuronal cultures. We first observe that the power spectrum can be used as a signature of the state of the network, for instance when inhibition is active or silent, as well as a measure of the network's connectivity strength. Second, the power spectrum identifies prominent developmental changes in the network such as GABAA switch. And third, the analysis of the spatial distribution of the spectral density, in experiments with a controlled disintegration of the network through CNQX, an AMPA-glutamate receptor antagonist in excitatory neurons, reveals the existence of communities of strongly connected, highly active neurons that display synchronous oscillations. Our work illustrates the interest of spectral analysis for the study of in vitro networks, and its potential use as a network-state indicator, for instance to compare healthy and diseased neuronal networks.

Price rivalry in airline markets: A study of a successful strategy of a network carrier against a low-cost carrier

Competition in airline markets may be tough. In this context, network carriers have two alternative strategies to compete with low-cost carriers. First, they may establish a low-cost subsidiary. Second, they may try to reduce costs using the main brand. This paper examines a successful strategy of the first type implemented by Iberia in the Spanish domestic market. Our analysis of data and the estimation of a pricing equation show that Iberia has been able to charge lower prices than rivals with its low-cost subsidiary. The pricing policy of the Spanish network carrier has been particularly aggressive in less dense routes and shorter routes.

Experimental evaluation of anonymous protocols under the JXTA middleware

JXTA is a peer-to-peer (P2P) middleware whichhas undergone successive iterations through its 10 years of history, slowly incorporating a security baseline that may cater to different applications and services. However, in order to appeal to a broader set of secure scenarios, it would be interesting to take into consideration more advanced capabilities, such as anonymity.There are several proposals on anonymous protocols that can be applied in the context of a P2P network, but it is necessary to be able to choose the right one given each application¿s needs. In this paper, we provide an experimental evaluation of two relevant protocols, each one belonging to a different category of approaches to anonymity: unimessage and split message. Webase our analysis on two scenarios, with stable and non-stable peers, and three metrics: round trip-time (RTT), node processing time and reliability.

Population-based incidence of myeloid malignancies: fifteen years of epidemiological data in the province of Girona, Spain

Myeloid malignancies (MMs) are a heterogeneous group of hematologic malignancies presenting different incidence, prognosis and survival.1–3 Changing classifications (FAB 1994, WHO 2001 and WHO 2008) and few available epidemiological data complicate incidence comparisons.4,5 Taking this into account, the aims of the present study were: a) to calculate the incidence rates and trends of MMs in the Province of Girona, northeastern Spain, between 1994 and 2008 according to the WHO 2001 classification; and b) to predict the number of MMs cases in Spain during 2013. Data were extracted from the population-based Girona Cancer Registry (GCR) located in the north-east of Catalonia, Spain, and covering a population of 731,864 inhabitants (2008 census). Cases were registered according to the rules of the European Network for Cancer Registries and the Manual for Coding and Reporting Haematological Malignancies (HAEMACARE project). To ensure the complete coverage of MMs in the GCR, and especially myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS), a retrospective search was performed. The ICD-O-2 (1990) codes were converted into their corresponding ICD-O-3 (2000) codes, including MDS, polycythemia vera (PV) and essential thrombocythemia (ET) as malignant diseases. Results of crude rate (CR) and European standardized incidence rate (ASRE) were expressed per 100,000 inhabitants/year

Predictive and distributed routing balancing (PR-DRB): high speed interconnection networks

Current parallel applications running on clusters require the use of an interconnection network to perform communications among all computing nodes available. Imbalance of communications can produce network congestion, reducing throughput and increasing latency, degrading the overall system performance. On the other hand, parallel applications running on these networks posses representative stages which allow their characterization, as well as repetitive behavior that can be identified on the basis of this characterization. This work presents the Predictive and Distributed Routing Balancing (PR-DRB), a new method developed to gradually control network congestion, based on paths expansion, traffic distribution and effective traffic load, in order to maintain low latency values. PR-DRB monitors messages latencies on intermediate routers, makes decisions about alternative paths and record communication pattern information encountered during congestion situation. Based on the concept of applications repetitiveness, best solution recorded are reapplied when saved communication pattern re-appears. Traffic congestion experiments were conducted in order to evaluate the performance of the method, and improvements were observed.