Molecular epidemiology is a science which utilizes molecular biology to define the distribution of disease in a population (descriptive epidemiology) and relies heavily on integration of traditional  epidemiological approaches to identify the etiological determinants of this distribution. The study of viral pathogens of aquaculture has provided many exciting opportunities to apply such tools. This review considers the extent to which molecular epidemiological studies have contributed to better understanding and control of disease in aquaculture, drawing on examples of viral diseases of salmonid fish of commercial significance including viral haemorrhagic septicaemia virus (VHSV), salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV). Significant outcomes of molecular epidemiological studies include:Improved taxonomic classification of virusesA better understanding of the natural distribution of virusesAn improved understanding of the origins of viral pathogens in aquacultureAn improved understanding of the risks of translocation of pathogens outwith their natural host rangeAn increased ability to trace the source of new disease outbreaksDevelopment of a basis for ensuring development of appropriate diagnostic toolsAn ability to classify isolates and thus target future research aimed at better understanding biological functionWhile molecular epidemiological studies have no doubt already made a significant contribution in these areas, the advent of new technologies such as pyrosequencing heralds a quantum leap in the ability to generate descriptive molecular sequence data. The ability of molecular epidemiology to fulfil its potential to translate complex disease pathways into relevant fish health policy is thus unlikely to be limited by the generation of descriptive molecular markers. More likely, full realisation of the potential to better explain viral transmission pathways will be dependent on the ability to assimilate and analyse knowledge from a range of more traditional information sources. The development of methods to systematically record and share such epidemiologically important information thus represents a major challenge for fish health professionals in making the best future use of molecular data in supporting fish health policy and disease control. Epidemiology, or the study of factors affecting the health of populations is as old as science itself, with Hippocrates (460-377 BC) being the first to examine the relationship between disease occurrence and environmental issues. More recent technological developments have facilitated the identification and exploitation of molecular biomarkers, whose use alongside traditional epidemiological approaches has led to a better understanding of the underlying mechanisms of disease transmission in populations. This young science of "molecular epidemiology" has emerged since the 1970s when the term was first coined in relation to the study of influenza virus [Descriptive molecular epidemiology most often involves an attempt at establishing the evolutionary history of a given viral species called its phylogeny. A phylogenetic tree is a graphical summary of this inferred evolutionary relationship between isolates from which the pattern and in some cases timing of events that occurred as viruses diversified can be hypothesised. Since all life is related by common ancestry, viruses (or other organisms) in current circulation display genetic diversity which reflects their evolutionary history due to the accumulation and inheritance of mutations when genetic material is copied. In the absence of historical information or isolates, which are often unavailable, the evolutionary history of viruses in current circulation can be hypothesised based on the sampling of current genetic markers and by working backwards to infer the most likely series of events which best explain the observed relationships. Fundamental to reconstructing such an evolutionary history is the comparison of homologous characters (often nucleotide or amino acid sequence positions); i.e. those which descend from a common ancestor. In practice, this involves creating an alignment of sequences which represents a hypothesis of positional homology and provides the basis for reconstructing evolutionary history based on a mathematical model of evolution. This review aims to focus on the contribution that the application of such descriptive tools has made to the practical understanding and control of viruses of salmonid aquaculture, rather than the techniques themselves, which have been extensively reviewed by others (e.g. ).Analytical epidemiology is based on observations of disease trends and incidence in different populations that turn into testable hypotheses, and entails rigorous collection of data for all aspects of study . As note8 viruses/mL in coastal seawater [Fish, unlike many other domestically reared farmed animals, are most often reared in open systems (cages) where they are exposed to a wide diversity of naturally occurring environmental pathogens. Recent estimates suggest the presence of a staggering 10seawater . Althougseawater , most arseawater . Whilst seawater , some viseawater ). Indeedseawater . Howeverseawater , and disseawater ,15.The advent of intensive fish husbandry and associated international movements of fish has fundamentally altered the natural equilibrium by exposing animals to new environments and their viruses to new host species . As a coThe accumulation of relatively high levels of genetic variation in viruses associated with aquaculture provides excellent and exciting opportunities for understanding the relative contribution of molecular epidemiology to their understanding and control. In order to identify the extent to which this capacity has been exploited in this field, this review focuses on three of the most significant and well studied RNA pathogens of salmonid aquaculture, viral haemorrhagic septicaemia virus (VHSV), infectious salmon anaemia virus (ISAV) and salmonid alphavirus (SAV). In this area the application of molecular epidemiology has provided important new knowledge of fundamental importance to disease management and control in the following key areas:• Viral taxonomy and classification• Understanding origins of diseases of aquaculture• Viral phylogeography and risks associated with viral translocation• Outbreak tracing and disease control• Genetic diversity and viral surveillanceViral haemorrhagic septicaemia (VHS) was, until the late 1980s thought to be a disease exclusive to the freshwater rainbow trout industry of Continental Europe, which is characterised by extensive degeneration and necrosis of the internal tissues . The disRhabdoviridae based on the distinctive morphology of viral particles in electron micrographs. Until relatively recently, insufficient data existed to assign any of the fish rhabdoviruses to novel genera with tentative groupings of "unassigned" and "vesiculovirus-like" viruses being proposed based on protein electrophoretic data and antigenic relatedness [novirhabdovirus) [VHSV is one of several important fish viral species that were originally identified as belonging to the family atedness . Sequencatedness . This diatedness . Indeed,dovirus) . TaxonomTo date, four main genetic groups of VHSV are recognised worldwide ,31, as dVHS was traditionally thought to be a disease exclusive to freshwater rainbow trout farming, where it has historically been responsible for significant economic loss. The first and subsequent identification of marine isolates of VHSV virus of differing genetic type in Europe  and NortUntil recently, only the adaptation of marine Genotype I strains of VHSV in rainbow trout had been shown to occur. Much like the Genotype Ib marine isolates, other naturally occurring genotypes of VHSV have been experimentally shown to be of low virulence to rainbow trout . The recWhile the above examples assume the input and subsequent adaptation of naturally non-pathogenic viruses in aquaculture systems, naturally occurring viruses can in some cases also cause disease without requirement for change. Following outbreaks of disease in marine farmed turbot in the British Isles caused by VHSV , experimUnderstanding the phylogenetic relationships between VHSV isolates highlights the existence of major viral genotypes confined largely to different geographical areas as discussed above. The physical separation of these areas has resulted in limited geneflow and independent evolution of the viruses circulating in these regions. It stands to reason that VHS viruses in these regions have not evolved independently but have rather co-evolved with their hosts to ensure continued survival. Since viruses rely on the availabilty of hosts to avoid extinction it is perhaps not surprising to find many examples where viruses within their natural range do not cause disease in their hosts. Anthropogenic factors, including those associated with international aquaculture, have in general lead to the increased potential for VHSV viruses to be translocated outwith their naturally occurring range. An extreme example of the potential consequence of such occurrence is that of the recent series of VHS epidemics in the Great Lakes region of North America. This series of epidemics, which spread rapidly through the region and resulted in dramatic fish kills, was shown to have been caused by a virus whose natural range appeared to be marine species inhabiting the eastern coastal areas of the USA or Canada . The intMolecular epidemiology is a powerful tool, which alongside more traditional epidemiological tools has potential for tracing the origins and spread of new disease outbreaks. Such an approach relies not only on the availability of large genetic datasets relating to phylogenetically informative and defined regions of the genome but also on availability of data relating to potential epidemiological contact. The latter is often more challenging to obtain. An example of the application and potential of such tools is the recent occurrence of VHS disease in rainbow trout in the British Isles, which until this point had a history of freedom from VHS. The disease was first identified and contained on a farm in North Yorkshire, England in May 2006 and initial investigations into the likely origin of introduction proved inconclusive. Subsequent molecular epidemiological analysis of the causative virus identified a Genotype Ia virus which was very similar to isolates from Denmark and Germany circulating between 2004 and 2006 and suggested likely introduction from this region . HoweverUnderstanding the natural sequence variation and divergence among isolates is of fundamental importance to ensuring adoption of an appropriate surveillance regime for VHSV and in interpretation of its results. Molecular detection methods such as real-time PCR are increasing being employed in this field due to benefits including sensitivity, specificity, high throughput, ease of interpretation and ability to include appropriate controls. Molecular methods rely on the specificity of primers and probes to ensure detection of their intended targets. Targetting such methods to the required well characterised and conserved regions of the genome thus requires a thorough knowledge of molecular variation of the species. Even with this knowledge, the risk that highly specific single-plex assays such as probe-based real-time PCR could fail to detect new emerging variants of pathogens should be recognised. Such methods as developed for VHSV have to date, however, proven to be robust in detecting all known variants of the virus in known circulation .Since phenotypic properties of viruses may in some cases be consistent with genetic origin, selecting isolates representative of the different genotypes can be a sensible strategy for further research into establishing their biological properties. Previous work on VHSV has investigated the consistency of pathogenic properties of different genotypes for different species ,50. SeleSalmonid alphaviruses are responsible for salmon pancreas disease (SPD) and sleeping disease (SD) conditions, primarily of farmed Atlantic salmon and rainbow trout, respectively. Clinical signs associated with SPD include abnormal swimming behaviour and lack of appetite, while characteristic histopathological signs include severe degeneration of exocrine pancreas, cardiomyopathy and skeletal myopathy . SD invoalphaviridae in the family Togaviridae, and differ markedly from the previously established New World viruses of Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus and the Old World viruses of Aura and Sindbis virus [Molecular analyses of salmonid alphaviruses have recently demonstrated that they represent a group of viruses within the genus is virus . Salmon is virus .Classification in this way can give clues as to the potential biological properties and functions of salmonid alphaviruses based on the established properties of their better studied relatives. Interestingly, most alphavirus lifecycles involve an obligate, commonly arthropod intermediate host. Such an intermediate host does not appear to be a requirement of salmonid alphavirus transmission since these viruses have been shown to efficiently transmit horizontally via direct water-borne transmission . WhetherThe most comprehensive molecular epidemiological analysis of the genetic relationships within the salmonid alphaviruses was recently conducted by Fringuelli et al. . This reLimanda limanda) and plaice (Pleuronectes platessa) [The monophyletic nature of the freshwater rainbow trout subtype of SAV  . The ideMolecular epidemiology has been applied to the study of SAV and has provided evidence to support farm to farm transmission in both Scotland and Ireland where clusters of identical sequences from isolates from different farms located within the same bodies of water have been demonstrated . FurtherKnowledge of molecular epidemiology and genetic diversity of SAV has led to the development of sensitive and specific molecular diagnostic methods  capable Infectious salmon anaemia (ISA) is a disease of farmed Atlantic salmon that has been responsible for extensive losses in all major regions where this species is farmed including, Norway, Canada, Scotland, the Faroe Islands and Chile. The disease is characterised by severe anaemia, ascites and haemorrhagic liver necrosis and congestion . While cMolecular epidemiological study has made a significant contribution to our understanding of ISAV. Following identification and initial characterisation, the virus was recognised as an orthomyxovirus , and ultNorth American and European evolutionary lineages of ISAV appear to have been present and diverged long before the development of commercial Atlantic salmon aquaculture . InteresMolecular epidemiogical study has been applied to understanding the appearance of ISA in Chile , which hMolecular detection methodologies have been developed to cover the broad range of ISAV viruses in global circulation , providiThe application of molecular epidemiology to the study of fish viruses has to date largely focussed on the use of descriptive techniques and interpretation of genetic relationships has often been hampered by a lack of associated analytical epidemiological information. The development of next generation sequencing technology promises a revolution in the ability to generate sequence data and thus information of potential epidemiological relevance. Descriptive molecular data alone is, however, inadequate in tracing pathogen spread, especially when variation is limited and evolution does not occur in a clock-like or regular fashion. The ability of molecular epidemiology to fulfil its potential to translate complex disease pathways into relevant fish health policy is thus unlikely to be limited by the generation of descriptive molecular markers. More likely, full realisation of the potential to better explain viral transmission pathways will be dependent on the ability to assimilate and analyse knowledge from a range of more traditional information sources. The development of methods to systematically record and share such epidemiologically important information thus represents a major challenge for fish health professionals in making the best future use of molecular data in supporting fish health policy and disease control.Making best use of this generated data to better understand the molecular basis of virulence also remains an important area for future research. Significant progress has been made in developing reverse genetic approaches for fish viruses (for review see ) which oDespite the limitations in available knowledge, molecular epidemiology has led to an improved understanding of the origins and spread of viruses in aquaculture and wild fish, which in turn has lead to significant practical improvements in disease management strategies and policy. A common theme in the examples explored seems to be the prevalence of probably benign viruses in the environment, which undergo an adaptation in association with aquaculture, where they adopt a pathogenic lifestyle. Major challenges for sustainable aquaculture are to manage the risk associated with such occurrence by reducing the opportunity for pathogens to reside and thus potentially adapt within aquaculture systems, coupled to their rapid identification and containment following disease emergence. Both these factors can be facilitated through implementation of biosecurity measures and the use of synchonous fallowing strategies to break potential long term cycles of infection and ensure rapid and appropriate containment of disease in discrete management areas. The implementation of surveillance programs based on the best available molecular epidemiological information offers great potential to support such measures in further developing a healthy and sustainable aquaculture industry that is necessary to satisfy an increasing world demand for cultured fish products.The author declares that they have no competing interests.


A biobank is a depository for biomaterials from a representative portion of a human population and acts as a vault with intricate detailed information pertaining to the individuals from whom biological materials have been collected. Biobanks can be classified into population biobanks, biobanks for molecular epidemiology and biobanks for disease biology.RGCB has been involved in biobanking with respect to three large studies in India namely i)Molecular Epidemiology of HPV in India, ii) A Randomized 2 versus 3 dose HPV Vaccination Clinical trial and iii) HPV AHEAD- : Role of Human Papilloma Virus Infection and other co-factors in the aetiology of Head & Neck Cancer.A cervical cytology biobank has been established at the centre which is an almost inexhaustible resource for fundamental and applied biological research. It helps to understand the natural history of HPV infection and HPV induced lesions and cancers, screening effectiveness, exploration of new biomarkers, surveillance of the short- and long-term effects of the introduction of HPV vaccination. However legal and ethical principles concerning personal integrity and data safety must be respected strictly and biobank based studies require approval of ethical review boards.The HPV vaccination study involves 10 different sites & different collaborating institutes across the country and all samples are shipped to RGCB, Trivandrum, which acts as a Central storage facility/ biobank. Sample shipment was an important procedure involving communication between base laboratory and biobank, import of registration database, strict temperature control, tracking of shipment and ready storage freezers on arrival. The sample verification process involves a temperature logger, freeze control tubes and bar code verification. The amount of clinical data linked to the samples determinate the availability and biological value of the sample. Thus acquiring the background information of each sample and cataloguing the available information systematically and meticulously is a must.The major problems faced in the management of cervical cytology biobanks have been reclassification of smears before entry into database, failure of temperature logger, bar codes slipping off and maintaining uninterrupted power supply.Publicly funded biobanks aim to promote the development of new knowledge by giving the research community access to data and samples. The most efficient way to acquire these benefits is to first maximize the use of biobanks in research and, second, to maximize the dissemination of knowledge developed by the research projects that used the biobanks. However there are issues with regard to the use of such stored materials especially when the demand occurs from the private sector. The decision is finally made by a scientific management committee consisting of members of World Health Organization (WHO) and the international agency for research on cancer (IARC).


Half a billion years ago, the first four-legged land animal crawled out of the sea onto dry land. How did the limbs that creature crawled on evolve from the fins of its fishy ancestors? This question has long intrigued biologists.PLOS Biology article, Denis Duboule, Joost M. Woltering, and colleagues shed new light on these questions from a comparative analysis of the regulatory mechanisms that control when and where certain members of the Hox gene family are turned on and off in zebrafish fins and mouse limbs.Fossil records suggest that tetrapod legs evolved step by step from fins, and comparative gene expression studies have provided some insights into how mutation and natural selection derived long limb bones from fin precursors. But the evolutionary path that lies between the structural elements  of fish fins and the toes and fingers of tetrapod digits has remained obscured. Are tetrapod digits homologous to fish radials? Did the genetic capacity for digit differentiation exist in fish ancestors, or is it unique to tetrapods? In their recent HoxA and HoxD, are known to function in patterning the developing vertebrate limb. In land animals, but not in fish, HoxD has what is known as a “bimodal expression pattern,” meaning that one subset of Hoxd genes directs the development of the long bones on the proximal (body) side of the wrist or ankle, while another subset directs the development of the long bones on the distal side . This bimodal expression pattern is due to the preferential interaction of the 3′ and 5′ genes in these Hox clusters with flanking regions of DNA on their own side of the cluster. These flanking regions contain non-genic DNA in which are located so-called enhancers—DNA loci that control the transcription of genes. On the 3′ side of the HoxA and Hox D clusters sit the proximal enhancers, which regulate the expression of proximal genes in the cluster in the proximal part of the limb, and on the 5′ side are the distal enhancers, which regulate the expression of distal genes in the cluster, leading to the segregated pattern of 3′ and 5′ genes. Duboule and colleagues decided to find out whether the HoxA cluster shares this regulatory characteristic with HoxD, reasoning that if it does, that the bimodality arose before the Hox clusters duplicated, indicating also that the regulatory capacity to form digits was in place before land animals' evolutionary emergence from the sea. Such a finding would lend strength to the argument for homology between digits and fin radials.Two Hox gene clusters, Hoxa genes in mouse embryos and by comparing them with the expression patterns of Hoxd genes, the researchers determined that the HoxA gene cluster does indeed exhibit biomodality, with one regulatory module directing the development of the digits and another orchestrating the development of the proximal segment of the limb. Although they noted some differences in the details of the bimodal expression of HoxA and HoxD genes, the researchers concluded that this pattern was common to both these Hox clusters and therefore predated the evolution of tetrapods from their fish ancestors.By looking at the expression patterns of HoxA and HoxD clusters share the bimodality that is associated with the differential regulation of the proximal and distal development of tetrapod limbs, is the same true of the Hox clusters that direct fin development in fish? By looking at the interaction profiles of Hox genes in zebrafish embryos, the researchers discovered a partitioning pattern similar to that seen in the mouse, in which Hox genes located at the edge of the clusters tended to interact more with their nearest flanking DNA regions while those in the middle of the cluster interacted with the flanking regions on both sides, confirming the existence of this bimodal pattern. Their findings support the idea that the chromatin structure that underlies this regulatory mechanism existed before the evolution of tetrapod limbs and that digits, therefore, may be homologous to distal fin structures in fish.If both HoxA and HoxD clusters, together with their flanking 5′ regions, into mice. Surprisingly, in the resulting transgenic mouse embryos, zebrafish Hox gene expression was specific to the proximal and not distal (digit-associated) developing limb tissues. On the basis of these findings, the authors conclude that the bimodal regulatory landscape that controls HoxA and HoxD expression was indeed in place before fish and tetrapods diverged, and that the subsequent evolution of novel enhancers allowed it to be repurposed to bring about the development of tetrapod digits.The team then inserted (in separate experiments) zebrafish Returning to the original question: does this make fin radials and digits homologous? That, the authors decided, depends on definitions. Their findings clearly demonstrate that fish have both the genes and the regulatory architecture needed to form digits. However, they also show that the development of digits depends on additional genetic alterations occurring in the context of that preexisting regulatory landscape. Duboule and colleagues suggest that although fish radials are not homologous to digits in the classical sense, biologists should consider thinking in terms of regulatory circuitries rather than expression patterns when considering whether traits have arisen from a common ancestral characteristic. Hox Loci and the Origin of Tetrapod DigitsWoltering JM, Noordermeer D, Leleu M, Duboule D (2014) Conservation and Divergence of Regulatory Strategies atdoi:10.1371/journal.pbio.1001773


Populus genome, the recently released Eucalyptus grandis genome and the concerted efforts towards the generation of genome sequences for spruces (Picea sp.) and pines (Pinus sp.) by several groups worldwide, are fueling a multitude of inter-disciplinary studies and applications in sustainable forest production and conservation. Time now calls for the integration of scientific fields with an increased sense of urgency for delivery of effective biotechnologies.Forest trees have unquestionably entered the genomic era. The updated version of the The IUFRO  Tree Biotechnology biannual conference has established a solid tradition for over 20 years as the official meeting of the IUFRO working group 2.04.06 – Molecular biology of forest trees. This conference has convened scientists and foresters interested in the genetics, genomics, molecular biology and physiology of forest trees, and the application of this knowledge to tree improvement and conservation. The Tree Biotechnology Conference has undoubtedly been the premiere international forum where the most cutting edge research in tree biotechnology developed both in academia and industry is presented. “From genomes to integration and delivery”, this was the theme chosen for the 2011 edition of the IUFRO Tree Biotechnology Conference, first time to be held in South America. Our intention was to promote a more integrated and applied dialogue on tree biotechnology and genomics, beyond the mainstream discussion of the fundamental advances on the genetic mechanisms that underlie tree phenotypes.In nine scientific sessions some of the current advances of genomics applied to forest conservation, tree physiology, stress response, molecular breeding, in vitro and propagation technologies, wood development and genetically modified (GM) trees were highlighted. With 340 registered participants, the Conference brought to Brazil most of the world’s brain power in forest tree genomics and biotechnology. An outstanding team of international scientists shared their results and visions on the present and future of this fast moving area of forest science, while a brilliant group of young scientist and students delivered a very energetic and diverse collection of high-quality scientific presentations. Forty two countries were represented at the Conference with almost 100 different laboratories from tens of Universities, research institutions and private companies.During the seven days of the Conference 26 invited lectures, 63 oral and 185 poster presentations were delivered, totaling 274 papers made available as extended abstracts into this BMC Proceedings supplement. The special workshop on the hot topic of “Genomic Selection in tree breeding” and the several reports on whole-genome studies, made this conference edition inaugurate a deliberate effort towards a better integration between the quantitative genomics, the “single-gene” and the system biology approaches to more efficiently unravel the complex relationships between genotypes and phenotypes in forest trees. A field trip to the forest plantations, nurseries and mill of VERACEL Cellulose was a definite highlight and a welcome break from the scientific sessions, providing an overview of some of the advances and challenges facing the translation of research into plantation forestry.In closing this introductory statement, acknowledgements are due to the outstanding financial support provided by the competitive grants of the Brazilian Ministry of Science and Technology through the National Research Council (CNPq) and the Ministry of Education through its agency for graduate studies (CAPES). Major support was also provided by EMBRAPA , and VERACEL Cellulose, the host organizations, together with an exceptional suite of private sponsors. Besides the organizations that backed this conference and an active Scientific Committee involved in abstract review a number of people were involved in the organization and logistics. The conference would not have been possible without the valuable contributions of all these players.Given the rewarding feedback received after the Conference, the original goal of providing an exceptional mix of science, social activities and field exploration in a relaxed atmosphere was truly accomplished. The IUFRO Tree Biotechnology Conference 2011 made a significant contribution to advance the forest biotechnology research community one step ahead on the challenging task of moving from gene and genome discoveries to the delivery of valuable technologies into sustainable forestry.


Felis catus subject. The interactions present in the simulated data were predicted with a high degree of accuracy, and when applied to the real neural data, the proposed method identified causal relationships between many of the recorded neurons. This paper proposes a novel method that successfully applies Granger causality to point process data, and has the potential to provide unique physiological insights when applied to neural spike trains.The ability to identify directional interactions that occur among multiple neurons in the brain is crucial to an understanding of how groups of neurons cooperate in order to generate specific brain functions. However, an optimal method of assessing these interactions has not been established. Granger causality has proven to be an effective method for the analysis of the directional interactions between multiple sets of continuous-valued data, but cannot be applied to neural spike train recordings due to their discrete nature. This paper proposes a point process framework that enables Granger causality to be applied to point process data such as neural spike trains. The proposed framework uses the point process likelihood function to relate a neuron's spiking probability to possible covariates, such as its own spiking history and the concurrent activity of simultaneously recorded neurons. Granger causality is assessed based on the relative reduction of the point process likelihood of one neuron obtained excluding one of its covariates compared to the likelihood obtained using all of its covariates. The method was tested on simulated data, and then applied to neural activity recorded from the primary motor cortex (MI) of a  Recent advances in multiple-electrode recording have made it possible to record the activities of multiple neurons simultaneously. This provides an opportunity to study how groups of neurons form functional ensembles as different brain areas perform their various functions. However, most of the methods that attempt to identify associations between neurons provide little insight into the directional nature of the interactions that they detect. Recently, Granger causality has proven to be an efficient method to infer causal relationships between sets of continuous-valued data, but cannot be directly applied to point process data such as neural spike trains. Here, we propose a novel and successful attempt to expand the application of Granger causality to point process data. The proposed method performed well with simulated data, and was then applied to real experimental data recorded from sets of simultaneously recorded neurons from the primary motor cortex. The results of the real data analysis suggest that the proposed method has the potential to provide unique neurophysiological insights about network properties in the cortex that have not been possible with other contemporary methods of functional interaction detection. Neurons in the brain are known to exert measurable, directional influences on the firing activities of surrounding neurons, and a detailed analysis of these interactions improves our understanding of how the brain performs specific functions Granger causality has proven to be an effective method for the investigation of directional relationships between continuous-valued signals in many applications To address these issues, this paper proposes a point process framework for assessing Granger causality between multiple neurons. The spiking activity of each neuron is simultaneously affected by multiple covariates such as its own spiking history and the concurrent ensemble activity of other neurons. The effect of these factors on a neuron's spiking activity is characterized by a statistical framework based on the point process likelihood function, which relates the neuron's spiking probability to the covariates The proposed framework was used in an attempt to identify the causal relationships between simulated spike train data, and accurately estimated the underlying causal networks presented in the simulations. It was also applied to real neural data recorded from the cat primary motor cortex (MI) in order to assess the causal relationships that occur between multiple simultaneously recorded neurons during performance of a movement task.The experiments that were performed for the collection of real neural spiking data were approved by the Animal Ethics Committee of the University of Western Australia, and the National Health and Medical Research Council of Australia (NH&MRC) guidelines for the use of animals in experiments were followed throughout.Statistical analysis of the potential causal relationships between neurons was performed based on a point process likelihood function. The likelihood function related a neuron's spiking probability to possible covariates, such as its own spiking history and the concurrent activity of all simultaneously recorded neurons. The causal relationships between associated neurons were assessed based on the point process likelihood ratio, which represents the extent to which the likelihood of one neuron is reduced by the exclusion of one of its covariates, compared with the likelihood if all of the available covariates are used. The Granger causality measure based on the point process likelihood ratio also enabled us to detect significant causal relationship through a hypothesis testing based on the likelihood ratio statistic.A point process is a time series of discrete events that occur in continuous time To model the effect of its own and ensemble's spiking histories on the current spiking activity of a neuron, a GLM framework is often used to model the CIF. In the GLM framework, the logarithm of the CIF is modeled as a linear combination of the functions of the covariates that describe the neural activity dependencies A point process likelihood function was used to fit the parametric CIF and analyze Granger causality between neurons since it is a primary tool used in constructing statistical models and has several optimality properties Given the ensemble spiking activity in The Granger causality matrix We can test In any attempt to identify the causal relationships between multiple neurons simultaneously, the total number of the possible causal interactions to be investigated is usually large. Thus, the use of common statistical thresholds cited above to assess the causal interactions would lead to an unacceptably large number of false causal interactions  where the null hypothesis is incorrectly rejected Combining the multiple hypothesis testing results with the sign of In order to evaluate the proposed framework's ability to identify Granger causality for ensemble spiking activity, we analyzed synthetically generated spike train data. Simulated spike train data were synthetically generated based on the nine-neuron network of In order to select a model for each neuron we fit several models with different history durations Based on the estimated model, two kinds of causality maps were obtained using the proposed method. Firstly, the Granger causality map The FDR procedure was used as a solution for the multiple comparisons problem when considering a set of statistical inferences simultaneously. When controlling the FDR at a specific significance level  seen in , each haTo illustrate the application of the proposed method to real spike train data, 15 neurons were simultaneously recorded from the cat MI shown in Using the AIC, an optimum model for each neuron is selected to minimize the criterion. The non-overlapping spike counting window The GOF of the estimated model is assessed by using the Kolmogorov-Smirnov (KS) plots The causal connectivity between the recorded neural spike train data was assessed using the proposed framework, and the results are illustrated in The estimated GLM parameters We proposed a point process framework for identifying causal relationships between simultaneously recorded multiple neural spike train data. Granger causality has proven to be an effective method to test causality between signals when using the MVAR model, but to date it has been used for continuous-valued data Other model-based methods for assessing the directional relationships between neurons have been recently developed Some of the neurons included in this analysis showed no evidence of either self-interaction, or interactions with other neurons. Although these neurons also had non-zero GLM parameters for self-interaction, as indicated with green asterisks in The identification of excitatory self-interactions for some of the analyzed neurons was an unexpected and interesting finding. Analysis of the spiking features of these neurons verified that they were not engaged in any manner of bursting behavior that may explain the self-excitation result. Based on the high history orders that were also seen in those neurons as shown in http://www.neurostat.mit.edu/gcpp).The Matlab software and the data sets used to implement the methods presented here are available at the website (


Various murine models are currently used to study acute and chronic pathological processes of the liver, and the efficacy of novel therapeutic regimens. The increasing availability of high-resolution small animal imaging modalities presents researchers with the opportunity to precisely identify and describe pathological processes of the liver. To meet the demands, the objective of this study was to provide a three-dimensional illustration of the macroscopic anatomical location of the murine liver lobes and hepatic vessels using small animal imaging modalities. We analysed micro-CT images of the murine liver by integrating additional information from the published literature to develop comprehensive illustrations of the macroscopic anatomical features of the murine liver and hepatic vasculature. As a result, we provide updated three-dimensional illustrations of the macroscopic anatomy of the murine liver and hepatic vessels using micro-CT. The information presented here provides researchers working in the field of experimental liver disease with a comprehensive, easily accessable overview of the macroscopic anatomy of the murine liver. Within the last twenty years the number of publications describing the use of mouse models has steadily increased. Animal models of human disease have become an integral part of virtually all areas of medical research. Consequently, various murine models of liver disease have been developed including models of inflammatory liver disease To gain a better understanding of the macroscopic anatomy of the murine liver and its associated microvasculature we compiled information from our own previous research in C57BL/6 mice using micro-CT and compared our observations to the literature.Micro-CT images were acquired as described recently Our literature search utilized, the search engines Medline, Google, and Vetseek Nomina Anatomica Veterinaria (NAV) which is the standard reference in veterinary science for anatomical terminology Searching Medline we found four articles describing the macroscopic anatomy of the murine liver In addition to the journal articles available online, we identified seven books that included a description of the murine liver anatomy During our literature search we found no articles or books that comprehensively reviewed the murine liver anatomy with regard to the classical slice orientations used in small animal in vivo-imaging, nor did we find any articles that described the adjacent liver vessels in this context.Impressio gastrica) of the caudal surface of the left lateral liver lobe is caused by the stomach, the right kidney lies within the renal impression  located on the caudal surface of the caudate lobe. Other impressions of the liver are the duodenal , oesophageal (Impressio esophagea), and the jejunal impression , which are difficult to identify in small animal imaging.The murine liver has a convex shaped cranial surface conforming to the vault of the diaphragm and a concave shaped caudal surface, which is adapted to the surface of the abdominal organs. While the gastric impression (Ligamentum coronarium) and the triangular ligament (Ligamentum triangulare sinistrum), respectively. According to the literature, mice have no ligaments stabilizing the right medial and right lateral liver lobe. On the right side, only the caudate process is fixed to the right kidney by the hepatorenal ligament . Ventrally, the falciforme ligament  containing the teres ligament (Ligamentum teres hepatis), is considered a relic of embryonic development rather than a ligament of fixation  and the left lateral lobe (red color-coding), with the smaller left medial lobe lying cranially and medially to the larger left lateral lobe , 2, 3, 4Similarly, the right liver lobe can be subdivided into the right medial lobe (blue color-coding), which is located directly below the diaphragm and lateral to the right side of the gall bladder, and the right lateral lobe (green color-coding), which is smaller and located more caudally than the right medial lobe.The caudate lobe is subdivided into the larger caudate process (cyan color-coding) and the smaller papillary process (magenta color-coding). The larger caudate process lies directly caudal to the right lateral lobe and overlaps the right kidney ventrally and laterally. The papillary process in general is relatively small, and can be subdivided into two smaller parts (no specific nomenclature exists for these two subdivided parts) and is located between the stomach, the right lateral lobe, and the caudal caval vein.Finally, the quadrate lobe is described in the NAV. This lobe is located at the medial edge of the left lateral lobe and is not further subdivided. While we have not been able to identify this small lobe of the liver macroscopically or with micro-CT images, other authors depicted the quadrate lobe in their schematic drawings without labeling it within the images While anatomical variations of the liver do exist both within and between different mouse strains, to date, we did not evaluate these differences in-depth. However, we observed variations in our own measurements at the fusion of the two middle lobes. This variation has been described, by Rauch et al. To compliment the anatomical description of the liver we also gathered additional information on the anatomical relations of the adjacent perihepatic organs and liver-related vessels.Only separated by the diaphragm, the heart and the lungs are cranial to the liver. While these organs are often easily distinguished from the liver, in one case we observed transdiaphragmatic herniation of the right medial liver lobe, which was clearly identifiable just after administration of a liver-specific contrast agent .Impressio renalis) of the liver. Between the medial cranial pole of the kidneys and the liver the triangularly shaped adrenal glands are located on both sides (Imressio gastrica) adjacent to the surface of the left lateral lobe, while the spleen is located between the left kidney, the stomach, and left abdominal wall.The half-moon shaped spleen can be found caudal to the liver, kidneys, adrenal glands, and stomach . As mentth sides . On the Arteria coeliaca; A. mesenterica cranialis, in humans the superior mesenteric artery) and among others branches into the hepatic artery which runs cranially. Due to the limitations of in vivo micro-CT of the hepatic artery we have been able to identify the proximal hepatic artery, but cannot trace this vessel into the liver. However, the branching pattern of the hepatic artery has been reported to correspond with the branching of the portal vein and the billiary ducts The coeliac artery (Ramus dexter) draining into the caudate process and the right lateral lobe (Ramus sinister). The left branch provides blood-flow into the right medial lobe and divides into the umbilical part  for the left medial lobe and the transversal part  for the left lateral lobe. The NAV provides no specific nomenclature for the small branch providing blood supply to the papillary process.The portal vein drains blood from the gastrointestinal tract and spleen to the liver. The portal vein divides into the right branch . For example, some authors described the caudate process (of the caudate lobe) as the caudate lobe Nomina Anatomica Veterinaria, which was introduced in 1955 and since then has continuously been updated by an international group of veterinarians. Regarding the murine liver lobes we found the NAV to serve almost perfectly (with the only exception that we found it difficult to identify the quadrate lobe). However, there were some problems in the most recent edition of the NAV from 2005 To overcome the problems that may arise from the inconsistent designation of the liver lobes we recommend using the nomenclature in accordance with the Photographs and schematic drawings are primarily used in virtually all other publications dealing with the anatomy of the murine liver. Although different three-dimensional mouse atlases are available in book form While our study aimed at providing a general overview of the macroscopic anatomy of the murine liver, we did not investigate differences related to mouse strain, gender, weight, or age. These differences, however, have to be considered when trying to refer to the anatomical descriptions presented in our manuscript.The provided three-dimensional illustrations of the macroscopic anatomy of the murine liver using micro-CT may promote clarity and precision among scientists and veterinarians working in the field of liver research and may be helpful as a reference for future experimental research in this field.


The global threat of antimicrobial resistance (AMR) needs to be addressed urgently. The global surveillance of AMR pathogens is patchy and limited by financial and technical constraints. Without an early-warning system, the emergence and spread of AMR often goes unnoticed until a given strain has become endemic.Enterobacteriaceae (CRE), we analyzed the potential role of the International Health Regulations (IHR), a legally binding agreement between 194 States Parties, whose aim is “to prevent, protect against, control and provide a public health response to the international spread of disease” with respect to AMR and assess whether selected CRE events fulfil the four criteria of Annex 2 of the IHR.Using the example of carbapenem-resistant Certain events marking the emergence and international spread of KPC and NDM-1-producing CRE fulfil the criteria for notifiability to WHO. This can be extrapolated to other types of AMR. At the same time, ambiguities in Annex 2 and limited specific WHO guidance may make notification decisions a matter of debate. Obstacles for the application of the IHR to AMR include a lack of capacities within WHO.The global threat posed by the spread of AMR requires a coordinated international response. Recognizing the applicability of the IHR to AMR could serve as a “wake-up call” and obligate WHO and States Parties to strengthen surveillance and response, which could in turn contribute to containing the spread of AMR and preserve the efficacy of antimicrobials. Although States Parties and WHO share a collective responsibility in the process, WHO must clearly delineate its position regarding AMR and the intended role of the IHR in this context.None declared.


The habit of removing the nails cuticles of hands and feet is a typical cultural practice in Brazil and can be an important factor for hepatitis B and C infection. We conducted a seroepidemiological survey of hepatitis B and C in professional manicures/pedicures in salons in Sao Paulo - Brazil, with the aim of estimating the prevalence of serological markers of HBV and HCV infection on manicures/pedicures; get to know the information level of that have about transmission routes and Prevention of Hepatitis B and C, evaluate the perception degree of risk exposure accidental infectious agents and check the use of biosafety norms in the work routine of these professionals.This is a descriptive, cross sectional prospective study. The survey involved 100 participants manicures/pedicures from beauty salons, by random drawing. An individual for information about the characteristics participants; simultaneously questionare has been applyed was blood collected sample for the detection of serological markers of HBV and HCV of each participant.Prevalence estimates were found in 8% of HBV and 2% of HCV. Membership biosafety standards for professionals were relatively low and inadequate. It was found that the degree of knowledge about routes of transmission, prevention, biosecurity standards and risk perception of infectious agents in their professional activity, was low. Manicures and pedicures are a group with increased risk factors, which determine a likely greater exposure to infection with viral hepatitis than the general population and all ways of prevention must be used to protect there health.It important to raise awareness manicures and pedicures becomes for the use of individual protection in their routine work to prevent future disease.None declared.


Recent research has elucidated several different mechanisms for acupuncture. However the inter-relationship between these mechanisms and how acupuncture affects complex physiological systems is still not understood. Heart rate variability (HRV), the beat-to-beat fluctuations in the rhythm of the heart, results from the regulation of the heart by the autonomic nervous system (ANS). Low HRV is associated with increased risk of all-cause mortality and is a marker for a wide range of diseases. Coherent HRV patterns are associated with increased synchronization between the two branches of the ANS, and when sustained for long periods of time result in increased synchronization and entrainment between multiple body systems. This presentation is a systematic review of the clinical trials that have been undertaken examining the effect of acupuncture on HRV and the implications for HRV representing a systems level mechanism for acupuncture.The literature was reviewed using Medline, Science Citation Index, Cochrane , the New England School of Acupuncture library databases, cross-reference of published data, personal libraries and Chinese medicine textbooks.Results from randomized placebo controlled trials strongly suggest that acupuncture can improve HRV, especially when acupuncture is delivered in clinically valid dosages to subjects with a medically diagnosed condition and with the inclusion of an inert placebo control.There is sufficient evidence in the literature to support the conclusion that acupuncture improves HRV. Acupuncture may function by mediating global physiological regulation through improvement of HRV and synchronization of the two branches of the ANS. As a complex intervention, such a view of acupuncture mechanism is conceptually aligned with systems and complexity theory and is more compatible with traditional East Asian medical theory.


While generating the stream of consciousness and driving our actions in the world the brain largely relies on implicit forms of information processing. Conscious and unconscious factors are closely coupled and can be seen as complementary since unconscious processing can be sensitive to regularities within signals prior to conscious awareness, suggesting that the content of consciousness can be biased by unconscious factors.In the context of the Distributed Adaptive Control (DAC) theory of the mind, brain and body nexus , we prevBuilding on an initial large scale model of thalamo-cortical dysrhythmia , the pre


The objective of this experimental study was to develop a new combination technique for electrode placement and the histomorphological evaluation of its effectiveness for the electrochemical lysis of large intraocular tumours.The ECL was conducted on two freshly enucleated eyes containing large tumours, with maximal prominence of 11 and 12 mm and maximal base diameter of 16 and 19 mm, respectively. The ECL was carried out using an ECU-300  apparatus generating an electrochemical charge of 30-35 K. In the course of the ECL procedure we used a new original combination technique of electrode placement, i.e., the anode was a surface electrode and the cathode was an intrastromal electrode. The anode had an original design.A greyscale B-scan performed after the ECL completion showed decreased echogenicity and heterogeneity of the echo-structure of the tumour. According to the bioimpedancemetry data, the average duration of the ECL session was from 20 to 30 minutes depending on the tumour size. The results of pathomorphological examination performed after the ECL on two freshly enucleated eyes appeared to be similar. Thus, in both cases after lysis the eyeball did not change its size or shape. In both cases the tumour originated from the choroid plexus and showed subtotal necrosis. There was a pronounced boundary between the intact and electrochemically damaged tumour regions which attests to the local effect of the ECL restricted to the electrode placement area only.The growing interest in the ECL procedure is due not only to its availability and low cost but mainly to its real clinical effect demonstrated in numerous publications. The absence of a developed ECL technology for the treatment of intraocular tumors, and, hence, reports on its clinical effectiveness, gave us the impetus to conduct this study.The proposed ECL method is promising and can be considered as optional for the organ-sparing treatment of large-sized intraocular tumours. Further optimization of the ECL parameters, as well as the development of sets of surface and intrastromal electrodes for different types of tumours, is required. Choroidal melanoma (CM) is the most common primary malignant intraocular tumour that accounts for nearly 80% of all choroid plexus tumours. Owing to the high risk of metastases 3–16%) [6% 1–4],,4], the Nowadays, the preferred concept in ocular oncology for CM treatment is the use of organ-sparing methods which basically require radical surgery against the tumour while causing minimal damage to surrounding normal tissues.Currently, the range of organ-sparing methods available for CM treatment is wide enough and includes laser photocoagulation, brachytherapy, cryodestruction, transpupillary thermotherapy, photodynamic therapy, surgical resection of the tumour (en block resection), etc. .The possibility of the use of organ-sparing treatment of CM will largely depend on the tumour size  and location . Enucleation is performed to remove large-sized eye tumours.In view of the above, the development of new minimally invasive and organ-sparing methods for the treatment of large CMs  is becoming a topical issue.A good example of the organ-sparing trend in oncology is the electrochemical lysis (ECL) method which induces destructive chemical reactions occurring during direct current flow between two bipolar electrodes introduced into the tumour (HCl is produced at the anode and NaOH at the cathode), that subsequently results in tissue coagulation and colliquative necrosis around the electrodes.The ECL method has been fairly successfully used for the treatment of breast cancer, hepatic carcinoma, and tumour metastases in the liver, benign prostatic hyperplasia, cancer of oesophagus, lungs, pancreas, and skin –11.In general oncology, the standard ECL technique involves a parallel introduction of two or more needle electrodes into the tumour. Using a similar approach in ocular oncology, the electrodes should be introduced in the intraocular tumour ***transsclerally in the zone of projection of the tumour base onto the sclera. In order to obtain an adequate necrosis of large tumours, three or more electrodes must be introduced intrastromally and correctly positioned under ultrasound control  which is fraught with risks and several complications, such as iatrogenic retina tear, hemophthalmos, subretinal and subchoroidal haemorrhages, etc.Therefore, the problems with electrode placement and inability to predict the optimal electric field’s effect on the tumour make the search for new approaches to ECL application in ocular oncology a topical undertaking.The objective of this experimental study was to develop a new combination technique for electrode placement and the histomorphological evaluation of its effectiveness for the ECL of the large-sized intraocular tumours.The ECL was conducted on two freshly enucleated eyes containing the large-sized tumours, with maximal prominence of 11 and 12 mm and maximal base diameter of 16 and 19 mm, respectively.The ECL was carried out using the “ECU-300”  apparatus generating an electrochemical charge of 30–35 K. In the course of the ECL procedure, we used a new original combination technique of electrode placement, i.e., the anode was a surface electrode and the cathode was an intrastromal electrode. The anode had an original design: it was made of the platinum wire to form a round mesh of 9 mm in diameter and with a hole in the centre. The cathode was a needle electrode made of 0.5 mm platinum wire .At the ECL preparation step, we determined the boundaries of the tumour base projection onto the sclera by their marking with 1% water– alcohol solution of brilliant green. To perform the ECL, the anode was applied onto the sclera within previously marked boundaries of the tumour base and stitched with two interrupted sutures. The cathode was introduced perpendicularly to the sclera into the centre of the tumour base through the hole in the anode electrode. To introduce the cathode into the tumour, a trocar with a screw-type length adjustment and a 25-G cannula were used.The length of trocar was adjusted to accommodate the length of the extra-scleral part of the 25-G cannula + sclera thickness + electrode penetration depth into the tumour. Then, sclerotomy was performed using the trocar inserted into the lumen of the cannula, by inserting it to its full depth into the tumour perpendicularly to the sclera followed by trocar withdrawal from the lumen of the cannula and its replacement with the electrode of a predetermined length.The depth to which the electrode was inserted into the tumour had been determined in advance based on the results of previous ultrasonic scanning  by subtracting 1.5–2 mm from the value of the maximum prominence in the centre of the tumour. The length of the electrode active part was calculated in the same manner as the trocar length .The active positioning of the intrastromal electrode was carried out in the course of surgery under the trans-corneal and trans-scleral ultrasound control using a 10-MHz probe of the Ultrascan  apparatus.Z) was conducted in an automated mode, and the software produced the chart of changes of tissue resistance in real-time (Z) flattened out and appeared to be hardly affected by time, it was an indication for completion of the ECL procedure.To evaluate the ECL effectiveness, we used the bioimpedancemetry method which is the measurement of total electrical resistance of tumour tissue placed between two electrodes in the direct electric field of variable frequency. Multiple impedance measurements of lysed tissue in the course of ECL were performed using an experimental setup at 2 and 10 kHz. To this end, the ECL procedure was interrupted every 3 min for 1–2 s. The same electrodes were used for both ECL and bioimpedancemetry. Impedance measurement . In the centre of the area there was a canal resulted from the insertion of the intrastromal electrode (cathode), its opening containing dark fluid expelled after the electrode withdrawal. When the eyeball was cut open, the impurity-free liquid of the vitreous body leaked out through the base of the tumour. The location of eye integuments and tumour was in accord with the results of clinical and instrumental examination. On section, the tumour is dark and has small slit-shaped spaces through which a slightly frothy, gel-like liquid, with admixture of reddish-brown, blood-tinged fluid, is oozing.In both cases the tumour was originated from the choroid plexus and showed subtotal necrosis.For the sake of convenience of description of the ECL-induced tumour morphological changes, the tumour was conditionally divided into three parts: the apex, middle part and periscleral part.The apex part showed necrosis with cell fragmentation, nucleus contractions and stiffing (caryopicnosis) and nucleus fragmentations (caryorexis), pigment condensation, appearance of slit-shaped spaces in place of the vessels filled with lysed blood and gaps along the contour of the palisade structures .The middle part demonstrated total cell necrosis. The contours of the gaps resemble those of individual cells and lumens of destroyed vessels . The sepIn the periscleral part of the tumour located next to the cathode canal the morphological picture resembled that of the middle part except for the smaller size cavities, owing to the absence of large vessels in this part of the tumour .The lumen of the canal formed after withdrawal of the intra-scleral cathode electrode) is filled with pigmented debris with an admixture of lysed blood .Given that the area of the surface electrode is smaller than the tumour base area, some periscleral spots of the intact tumour tissue have been found. These spots were characteristic for CM, i.e., they were intensively pigmented and composed mainly of spindle cell type A melanocytes which showed moderate polymorphism and minimal infiltration of the inner layers of the sclera.There was a pronounced boundary between the intact and electrochemically damaged tumour regions  which atThe growing interest in the ECL procedure is due not only to its availability and low cost but mainly to its real clinical effect demonstrated in numerous publications , 7–14.The absence of developed ECL technology for treatment of intraocular tumours, and, hence, reports on its clinical effectiveness, gave us the impetus to conduct this study.We set out to develop a new method making use of combination of the surface and intrastromal electrodes, as well as their original placement, which hitherto has never been described. To evaluate the ECL effectiveness, we performed the bioimpedancemetry of the ECL-treated tissues and morphological examinations of the large-sized intraocular tumours. The experiment was aimed at developing an integrated and manageable ECL method based on unbiased impedancemetry measurements, thus allowing the evaluation of its dynamics and determination of the point of its completion.The direct current flow between the electrodes results in tissue devitalization owing to its electrolysis. In the course of the ECL procedure the resistance of tissue (Z) positioned between the electrodes drops indicating the occurrence of tissue necrosis. The registration of therapeutic effect  is based on the impedancemetry measurements which are consistent and little changeable with time.The histological picture of the ECL-induced CM necrosis demonstrates different patterns of tumour destruction, primarily of its vessels, around each electrode depending on their polarity.Under the cathode electrode a pronounced vasodilatation and engorgement of large vessels occur accompanied by the capillary wall destruction and extensive hemorrhages into the necrotized tissue due to an increased turgor pressure caused by the electro-osmotic fluid flow. On the anode side the capillary reaction was only slightly noticeable. Therefore, the electromagnetic field effects in biological tissues are due to the obstruction of the microvascular bed. In the cathode region the capillaries are blocked owing to the electro-osmotic fluid flow, and in the anode region the pathological changes occur due to the micro-thrombotic events. Owing to the remote placement of the electromagnetic field source the final area of the ECL-induced tissue lesions must exceed the total area of primary necrosis.The presence of the periscleral sites of intact tumour separated by a pronounced boundary from the electrochemically damaged tumour spots indicates to the importance of the accurate placement of surface electrode, as well as its selection, taking into account the size of tumour base projection onto the sclera and avoiding the use of electrodes with smaller contact area.One of the particular features of ECL treatment of the intraocular tumours is the increased intraocular pressure occurred in the course of the ECL procedure. This is due to active gas bubble formation within the tumour and hampered evacuation of liquid debris via the electrode canal. Therefore, the removal of cell-free products of tumour necrosis using the vitreotom secures the maintenance of the original level of intraocular pressure, does not interfere with the ECL procedure and enables process stability owing to the replenishment of evacuated volume with BSS saline.The updated pattern of the electrode placement geometry using surface extrascleral and intrastromal electrodes and adherence to correct polarity while placing electrode in the tumour, opens up new horizons in achieving total intraocular tumour destruction. The design feature of this ECL technique is an individual selection of surface electrode which covers the whole tumour base over its projection onto the sclera, while a centrally positioned hole enables to introduce the intrastromal electrode to any depth allowing its placement maximally close to the tumour apex and preventing electrode dislocation within this position.When setting the parameters of ECL, we were guided by the charge value which would knowingly cause necrosis of a given tumour volume. This value was experimentally established to be 30 K per 1 cm3 of tumour tissue, and the increase of charge above this value does not practically cause the expansion of necrosis zone , 16. HowFurther modifications, refinement and customizing of the ECL method to address the specific needs of ophthalmologic oncology will allow the pre-modelling of tumour necrosis patterns aided by using the specifically designed software, and thus will help to achieve higher treatment effectiveness. Working out of the objective method of real-time assessment of pathologic changes occurring within the tumour, e.g., by measuring active and reactive tissue resistance by means of bio impedancemetry, provides the effective control and regulation of the ECL procedure.Also, the above method offers additional benefits in investigating tumour morphology and growth pattern, as the fine-needle aspiration biopsy of the intraocular tumour can be performed simultaneously with electrode insertion.Undoubtedly, the size of the intraocular tumour destruction occurred after clinical use of the ECL method will depend not only on the parameters of the procedure but also on the duration of the post-ECL time period. To elucidate these issues, the insightful information from clinical trials will be required.Our experimental study indicates that the new ECL method employing the original combination of electrode placement combines minimal tissue injury and complete tumour destruction under the area of electrode application. The use of surface electrode enables to direct and evoke destruction of the whole tumour base area.The combination of surface and intrastromal electrodes allows the minimal damage to the scleral integrity in the site of tumour base projection. Further experiments dealing with variations in depth of the intrastromal electrode insertion and the amount of current, coupled with bioimpedancemetry, will enable the regulation of morphological changes within the tumour.The proposed ECL method is promising and can be considered as optional for the organ-sparing treatment of large-sized intraocular tumours. Further optimization of the ECL parameters, as well as the development of sets of surface and intrastromal electrodes for different types of tumours, is required.


From climatology to biofluidics, the characterization of complex flows relies on computationally expensive kinematic and kinetic measurements. In addition, such big data are difficult to handle in real time, thereby hampering advancements in the area of flow control and distributed sensing. Here, we propose a novel framework for unsupervised characterization of flow patterns through nonlinear manifold learning. Specifically, we apply the isometric feature mapping (Isomap) to experimental video data of the wake past a circular cylinder from steady to turbulent flows. Without direct velocity measurements, we show that manifold topology is intrinsically related to flow regime and that Isomap global coordinates can unravel salient flow features. The characterization of complex flows is a major challenge in climatology, biology, and engineering Here, we propose the implementation of a machine learning framework for unsupervised characterization of fluid flows. Different from established flow visualization techniques that require a-posteriori intensive processing of high resolution images D positioned vertically at the cross-section of a water tunnel. A dye-injection system is developed for improved visualization of the flow streaklines around the cylinder through a digital camera (see the Methods for further details). We vary the flow regime by changing the free stream velocity, U.To demonstrate our approach, we study the flow past a circular cylinder by processing flow visualization video data with Isomap for Reynolds numbers ranging from 50 to 1725. For such range, the fluid experiences steady separation, the formation of regular vortex patterns , and the initiation of turbulence. We anticipate Isomap to detect flow regimes through varying dimensionality of the embedding manifolds, similarly to the problem of collective behavior of animal groups, where dimensionality is showed to relate with the degree of coordination between individuals In the framework of nonlinear machine learning, we regard experimental video frames as the Isomap ambient space and seek to characterize the flow by studying the embedding manifolds. We demonstrate that the topology of the embeddings can be associated with the flow regime, whereby lack of flow separation is manifested through one dimensional manifolds and the presence of coherent structures through higher dimensionality. Further, we show that manifold inspection can be used to estimate the frequency of vortex shedding and study flow pattern variations due to externally-induced perturbations.Re . The Reynolds number is defined as We process experimental video data recorded with a commercial camcorder with the Isomap algorithm and study the relationship between the topological features of the embedding manifolds and the flow regime, controlled by the Reynolds number We further find that the topology of the embedding is related to two major features underlying the experimental data set. Specifically, in the two dimensional projection in We quantify the vortex shedding frequency by inspection of the annular projections recovered for Re, the flow can be described through nearly one dimensional embeddings, which capture the translational motion in the video feed. On the other hand, as coherent structures are shed by the cylinder, data points are fit on higher dimensionality manifolds, which also account for the shape of the vortices. We observe that increasing the degree of turbulence of the flow corresponds to “hiding” periodic fluctuations in the flow. Indeed, Isomap captures the prevalently translational nature of the data.Our analysis of the dimensionality of Isomap embeddings demonstrates a close correspondence between the algorithm outputs and the flow physics. We further elucidate such relations by studying the residual variances for the first three dimensionalities of the data sets, which capture the vast majority of the experiments . The tunnel cross-section is The Isomap algorithm is a nonlinear manifold learning methodology for dimensionality reduction problems Construction of the neighbor graphto approximate the manifold. The elements of the set of vertices Computation of the graph geodesic matrixto approximate the geodesic of the manifold. Floyd's algorithm Approximation of the manifold distance bynearest neighbor distance. The matrix Computation of the projective variablesapplying the classical MDS on the matrixThe outputs of Isomap are the transformed data points on an embedding manifold for the input data set Experimental videos are decompressed into “.jpg” image files and sequences of The vectors of the residual variances for the first three embedding dimensionalities are plotted against the respective Vortex shedding frequency is evaluated for experiments conducted at


The study of structural and functional connectivity  and dynamics in spontaneous brain activity is a rapidly growing field of research . The exiHere, we extended a recent neurophysiologically realistic spiking-neuron model of spontaneous fMRI activity  to exhibIn the presence of noisy oscillations on the same order of magnitude as system delays, the temporal connectivity structure plays a role in shaping the functional network connectivity. By effectively decreasing strong synchronous inputs to nodes, the network is stabilized and the need for fine-tuning of global coupling reduced when compared to the absence of delays.