"Next-generation" Sequencing (NGS): The new genomic revolution

In the past 5 years "Next-generation" Sequencing (NGS) technologies have transformed genomics by delivering fast, inexpensive and accurate genomeinformation changing the way we think about scientific approaches in basic,applied and clinical research. The inexpensive production of large volumes ofsequence data is the main advantage over the automated Sanger method,making this new technology useful for many applications. In this chapter, a brieftechnical review of NGS technologies is given, along with the keys to NGSsuccess and a broad range of applications for NGS technologies.

Inferring the mode of origin of polyploid species from next-generation sequence data.

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.

Evaluation of Routing solution for Next Generation Open Platform

Verkkoon kytkettävien laitteiden määrä on lisääntynyt viime vuosina, joka luo tarpeen reitittimille ja niiden ominaisuuksille. On muodostunut uusi tarve laitteille, jotka voivat yhdistää erilaisia verkkoja toisiinsa. Tällaisen reitittimen rakentamiseen tarvitaan vakaa alusta. Tällaisella alustalla luodaan mahdollisuus kuormittaa järjestelmää ilman suuria ongelmia. Tällainen alusta on Open Platform, joka on suunniteltu tällaisille toiminnoille ja yhdessä oikeanlaisen verkkoratkaisun kanssa sitä voidaan käyttää sille suunnitellussa ympäristössä. Tämän diplomityön tarkoituksena on arvioida neljää eri reititysohjelmistoa ja kahta eri IP pinoa. Työssä käytetyt testit on suunniteltu arviointia varten ja niiden tarkoituksena on tuoda esille ohjelmistoissa esiintyvät viat ja ongelmat. Kaikki testit ovat samoja kaikille ohjelmille ja tehdään samassa ympäristössä. Testit analysoidaan niiden ajon jälkeen ja niiden tulosten avulla tehdään päätös mitä näistä ohjelmistoista tullaan käyttämään seuraavan sukupolven avoimella alustalla, joka tulee toimimaan Nokian Intelligent Service Nodessa. Tämä verkon laite toimii yhdyskäytävänäerilaisten verkkojen välillä.

New telecom services over next generation SDH

Our main aim in this report is to use Next generation SDH to solve the problem associated with the new telecom services. We have tried to analyze the different services and in this way identified some drawbacks which can be seen as hindrances in supporting these services. In this thesis we will first try to have idea of the past SDH technology and how the next generation SDH came into effect overriding the drawbacks of the past SDH technology. Our main concern throughout the report will be the way we can use next generation SDH to provide quality telecommunication services. In the section dealing with the telecommunication services through next generation SDH we will consider how we can transport Ethernet services through the Next generation SDH and what are the benefits to the customer and the service provider in using next generation SDH as a carrier. We will also see to improve to the ATM services through Next generation SDH. And finally towards the end I have identified some possible future work can be done in this area.

The Next Step: Darwin, Brontë, Fowles

The present article proposes Heathcliff and Sarah Woodruff as monstrous beings who reclaim their desire to be agent subjects in a society and a narrative which deny such a possibility. It would be possible to argue, however, that their monstrosity might be that of the unique specimen, the potential first stage towards the improvement of species through natural selection as theorized by Charles Darwin in 1859. The multiple references to Darwin’s study in the novel by JohnFowles demonstrate that such a theory could clarify what Sarah represents in the novel. In a retroactive manner, Darwinian theory might be used to understand what Heathcliff is, who Heathcliff is, and why he is the object of general animosity. It might be concluded that what is really monstrous about these twocharacters is that both are new specimens, avant la lèttre, and they occupy a space to which language has no access.

Analysis of the mitochondrial DNA of Schizophrenia patients by next generation sequencing

Mitochondrial DNA (mtDNA), a maternally inherited 16.6-Kb molecule crucial for energy production, is implicated in numerous human traits and disorders. It has been hypothesized that the presence of mutations in the mtDNA may contribute to the complex genetic basis of schizophreniadisease, due to the evidence of maternal inheritance and the presence of schizophrenia symptoms in patients affected of a mitochondrial disorder related to a mtDNA mutation. The present project aims to study the association of variants of mitochondrial DNA (mtDNA), and an increased risk of schizophrenia in a cohort of patients and controls from the same population. The entire mtDNA of 55 schizophrenia patients with an apparent maternal transmission of the disease and 38 controls was sequenced by Next Generation Sequencing (Ion Torrent PGM, Life Technologies) and compared to the reference sequence. The current method for establishing mtDNA haplotypes is Sanger sequencing, which is laborious, timeconsuming, and expensive. With the emergence of Next Generation Sequencing technologies, this sequencing process can be much more quickly and cost-efficiently. We have identified 14 variants that have not been previously reported. Two of them were missense variants: MTATP6 p.V113M and MTND5 p.F334L ,and also three variants encoding rRNA and one variant encoding tRNA. Not significant differences have been found in the number of variants between the two groups. We found that the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of the bioinformatics analysis and annotation step would be desirable to facilitate the application of NGS in mtDNA analysis.

Neurology and psychiatry: waking up to opportunities of sleep. : State of the art and clinical/research priorities for the next decade.

In recent years, evidence has emerged for a bidirectional relationship between sleep and neurological and psychiatric disorders. First, sleep-wake disorders (SWDs) are very common and may be the first/main manifestation of underlying neurological and psychiatric disorders. Secondly, SWDs may represent an independent risk factor for neuropsychiatric morbidities. Thirdly, sleep-wake function (SWF) may influence the course and outcome of neurological and psychiatric disorders. This review summarizes the most important research and clinical findings in the fields of neuropsychiatric sleep and circadian research and medicine, and discusses the promise they bear for the next decade. The findings herein summarize discussions conducted in a workshop with 26 European experts in these fields, and formulate specific future priorities for clinical practice and translational research. More generally, the conclusion emerging from this workshop is the recognition of a tremendous opportunity offered by our knowledge of SWF and SWDs that has unfortunately not yet entered as an important key factor in clinical practice, particularly in Europe. Strengthening pre-graduate and postgraduate teaching, creating academic multidisciplinary sleep-wake centres and simplifying diagnostic approaches of SWDs coupled with targeted treatment strategies yield enormous clinical benefits for these diseases.

Performance Management of a Next Generation Network

Today's communication networks consist of numerous interdependent network components. To manage these networks and to ensure their reliable and efficient operation to meet the increasing customer usability demands, extensive network management tools are required from the service provider. The goal of this study was to adapt the Next Generation Network (NGN) providing VoIP services within a performance oriented network management system. This study focuses only on NGN network and the project was implemented as an assignment of the Network Operations Center of Elisa Corporation. The theoretical part of this study introduces the network environment of the Elisa NGN platform: its components and used signalling protocols as well as other exploitable communication protocols. In addition, the Simple Network Management Protocol (SNMP) is closely examined since it is commonly used as the basis of IP (Internet Protocol) network management. Also some primary applications enabled by the NGN technology are introduced. The empirical part of this study contains a short overview of the implemented network performance management system and its properties. The most crucial monitored MIB modules, SNMP parameters and implemented performance measurements are described. The trap topology and the role of the traps for management of the NGN platform are considered and finally, the conclusion based on the several disquisitions is made supported with suggestions for future improvements.

Military crisis management in the next decade (2020-2030) : inducing consent or relying on compliance?

The most outstanding conceptual challenge of modern crisis management is the principle of consent. It is not a problem only at the operational level - it challenges the entire decision-making structures of crisis management operations. In post-cold war times and especially in the 21st century, there has been a transition from peacekeeping with limited size and scope towards large and complex peace operations. This shift has presented peace operations with a dilemma. How to balance between maintaining consent for peace operations, whilst being able to use military force to coerce those attempting to wreck peace processes? To address such a dilemma, this research aims to promote understanding, on what can be achieved by military crisis management operations (peace support operations) in the next decade. The research concentrates on the focal research question: Should military components induce consent or rely on the compliance of conflicting parties in crisis management operations of the next decade (2020 – 2030)? The focus is on military – political strategic level considerations, and especially on the time before political decisions to commit to a crisis management operation. This study does not focus on which actor or organisation should intervene. The framework of this thesis derives from the so called ‘peacebuilding space’, the scope of peace operations and spoiler theory. Feasibility of both peace enforcement and peacekeeping in countering future risk conditions are analysed in this framework. This future-orientated qualitative research uses the Delphi-method with a panel of national and international experts. Citation analysis supports identification of relevant reference material, which consists of contemporary literature, the Delphi-questionnaires and interviews. The research process followed three main stages. In the first stage, plausible future scenarios and risk conditions were identified with the Delphi-panel. In the second stage, operating environments for peace support operations were described and consequent hypotheses formulated. In the third stage, these hypotheses were tested on the Delphi-panel. The Delphi-panel is sufficiently wide and diverse to produce plausible yet different insights. The research design utilised specifically military crisis management and peace operations theories. This produced various and relevant normative considerations. Therefore, one may argue that this research; which is based on accepted contemporary theory, hypotheses derived thereof and utilising an expert panel, contributes to the realm of peace support operations. This research finds that some degree of peace enforcement will be feasible and necessary in at least the following risk conditions: failed governance; potential spillover of ethnic, religious, ideological conflict; vulnerability of strategic chokepoints and infrastructures in ungoverned spaces; as well as in territorial and extra-territorial border disputes. In addition, some form of peace enforcement is probably necessary in risk conditions pertaining to: extremism of marginalised groups; potential disputes over previously uninhabited and resource-rich territories; and interstate rivalry. Furthermore, this research finds that peacekeeping measures will be feasible and necessary in at least risk conditions pertaining to: potential spillover of ethnic, religious, ideological conflict; uncontrolled migration; consequences from environmental catastrophes or changes; territorial and extra-territorial border disputes; and potential disputes over previously uninhabited and resource-rich territories. These findings are all subject to both generic and case specific preconditions that must exist for a peace support operation. Some deductions could be derived from the research findings. Although some risk conditions may appear illogical, understanding the underlying logic of a conflict is fundamental to understanding transition in crisis management. Practitioners of crisis management should possess cognizance of such transition. They must understand how transition should occur from threat to safety, from conflict to stability – and so forth. Understanding transition is imperative for managing the dynamic evolution of preconditions, which begins at the outset of a peace support operation. Furthermore, it is pertinent that spoilers are defined from a peace process point of view. If spoilers are defined otherwise, it changes the nature of an operation towards war, where the logic is breaking the will of an enemy - and surrender. In peace support operations, the logic is different: actions towards spoilers are intended to cause transition towards consent - not defeat. Notwithstanding future developments, history continues to provide strategic education. However, the distinction is that the risk conditions occur in novel futures. Hence, lessons learned from the past should be fitted to the case at hand. This research shows compelling evidence that swaying between intervention optimism and pessimism is not substantiated. Both peace enforcement and peacekeeping are sine qua non for successful military crisis management in the next decade.