A Survey of Challenges for Runtime Verification from Advanced Application Domains (Beyond Software)

Runtime verification is an area of formal methods that studies the dynamic analysis of execution traces against formal specifications. Typically, the two main activities in runtime verification efforts are the process of creating monitors from specifications, and the algorithms for the evaluation of traces against the generated monitors. Other activities involve the instrumentation of the system to generate the trace and the communication between the system under analysis and the monitor. Most of the applications in runtime verification have been focused on the dynamic analysis of software, even though there are many more potential applications to other computational devices and target systems. In this paper we present a collection of challenges for runtime verification extracted from concrete application domains, focusing on the difficulties that must be overcome to tackle these specific challenges. The computational models that characterize these domains require to devise new techniques beyond the current state of the art in runtime verification

Adaptive radiation of Arctic charr (Salvelinus alpinus) in three Norwegian lakes - niche segregation, phenotypic and genetic variation

Å forstå hvordan økologiske og fysiske faktorer fører til opprinnelsen av nye arter, og hvilke faktorer som former ny intraspesifikk diversitet, er den “hellige gral” i evolusjonær biologi. Adaptiv radiasjon er den evolusjonære prosessen som kan føre til diversifisering av fenotyper og genotyper i ulike miljøer, og som kan splitte en forfaders form eller linje i nye former og arter. I den økologiske artsdannelsesprosessen vil lokal tilpasning gjennom naturlig seleksjon drive oppsplittingen av populasjoner, noe som vil føre til evolusjon av reproduktiv isolasjon og dermed dannelsen av nye økotyper, morfer, populasjoner og til slutt arter. Et godt eksempel på en polymorf art er røya (Salvelinus alpinus) som kan ha ulike nisjer (det vil si tilpasning til spesifikke abiotiske og biotiske forhold) i en innsjø. Spesialiseringen til en bestemt nisje kan favorisere divergensen mellom morfene, noe som kan lede til forskjeller i utseende, vekst, kjønnsmodning, gytetid og sted, og over tid utvikle reproduktive barrierer mellom morfene. Denne doktorgradsavhandlingen fokuserer på fenotypisk og genetisk divergens av røyemorfer. Hovedmålet er å undersøke nisjesegregering på trofisk nivå (det vil si diettvalg og habitatbruk), ved å studere morfologiske og genetiske forskjeller mellom røyemorfer fra tre forskjellige ferskvannsystemer i Norge (Tinnsjøen, Tårnvatn og Skøvatn). To røyemorfer ble funnet eksisterende sammen i Skøvatn, tre morfer i Tårnvatn, og fire i Tinnsjøen. To nye morfer ble funnet i Tinnsjøen og Skøvatn. Alle morfene viste forskjeller i livshistorie, genetikk, fenotype, diettvalg og habitatbruk. De fiskespisende morfene ernærte seg hovedsakelig av fisk, og ble funnet i den profundale delen av Tinnsjøen og Tårnvatn. Planktivore morfer spiste hovedsakelig dyreplankton, og ble funnet i flere ulike habitater i disse tre innsjøene. Livshistoriekarakterer og habitatbruk var lignende hos de småvokste dypvannsmorfene, men morfen i Skøvatn viste forskjeller i diettvalg sammenlignet med morfen fra Tårnvatn. Den nye dypvannsmorfen som ble funnet i den dypere delen av Tinnsjøen har likhetstrekk med hulefisk som hvitt skinn, underutviklede øyne og små hjerneregioner. Parallell evolusjon kan være en forklaring for likhetene som er funnet blant noen av morfene i disse tre ferskvannssystemene. Funnene viser hvordan seleksjonspress kan føre til lignende resultater i samme miljøer, der fenotypisk plastisitet også kan være en viktig mekanisme i tidlige stadier av nisjespesialisering. Disse morfene er sannsynligvis i en økologisk artsdannelsesprosess, der naturlig seleksjon spiller en viktig rolle i den adaptive divergensen av morfer, og bidrar til reproduktiv isolasjon. Adaptiv radiasjon kan forklare tilpasninger og diversitet hos den polymorfe røya i ulike vann.Abstract Understanding the ecological and physical factors driving the origin of species, and which ones are shaping new intraspecific diversity, are the “holy grail” of evolutionary biology. Adaptive radiation is the evolutionary process that can generate diversification of phenotypes and genotypes across different environments, differentiating a single ancestor into different forms and species. Under ecological speciation, local adaptation through natural selection drives the divergence of populations, evolving reproductive isolation and leading to the formation of new eco morphs, populations, and ultimately, species. A good example of polymorphic species is Arctic charr (Salvelinus alpinus), which has the flexibility to occupy different niches (i.e. a specific range of abiotic and biotic factors that a species has specialised) in a lake. For example, in fish, the specialisation into a specific niche can favour divergence among morphs, showing differences in morphology, growth, maturity, spawning time and site, developing reproductive barriers among the morphs. This thesis focuses on phenotypic and genetic divergence of Arctic charr morphs. The main objectives are to investigate trophic niche segregation (i.e. diet choice and habitat use), morphological and genetic differences among sympatric Arctic charr morphs from three different lakes in Norway (Tinnsjøen, Tårnvatn and Skøvatn). Two Arctic charr morphs were found coexisting in Lake Skøvatn, three morphs in Lake Tårnvatn and four morphs in Lake Tinnsjøen. Two novel morphs were found in Lake Tinnsjøen and Skøvatn. All morphs showed divergence in life history, genetics, phenotype, diet and habitat use. The piscivore morphs fed mainly on fish and were found in the profundal habitat of Lake Tinnsjøen and Tårnvatn. The planktivore morphs were feeding mainly on zooplankton, and were found across different habitats from these three lakes. Life-history traits and habitat use was similar among the small-sized profundal morphs, but the morph in Skøvatn presented differences in diet choice compared to the morph from Lake Tårnvatn. Finally, the Abyssal morph was found in the deepprofundal habitat in Lake Tinnsjøen, presenting similarities with cave fish such as white coloration, reduced eyes and small brain regions. Parallel evolution could be responsible for the similarities found among some of the Arctic charr morphs across these three lakes. These findings show how selection pressures can sometimes lead to similar outcomes in similar environments. However, phenotypic plasticity may also be an important component during the early stages of niche specialization. These morphs are likely under ecological speciation, where natural selection could play an important role in the adaptive divergence of morphs, contributing to reproductive isolation. Arctic charr polymorphism could be a case of adaptive radiation, explaining their diversity across different freshwater systems

The role of the transcription factor JAGGED in early floral organogenesis

Initiation of organ primordia from pools of undifferentiated cells requires coordinated cytoplasmic growth, oriented cell wall extension, and cell cycle progression. It is debated which of these processes are primary drivers for organ morphogenesis and directly targeted by developmental regulators. The single zinc finger transcription factor JAGGED (JAG) is a direct target of several floral organ identity genes and is expressed in early organ primordia (Dinneny et al., 2004; Ohno et al., 2004; Gomez et al., 2005; Kaufmann et al., 2009). Loss of function jag mutants have narrow floral organs with reduced distal growth. Quantitative 3D imaging has revealed that JAG is required for the transition from meristematic to organ primordium cell behaviour. The transition involves an increase in the rates of cell division and cell growth, a shift from isotropic to anisotropic growth, and modifications in cell size homeostasis in primordia (Schiessl et al., 2012). In this project, ChIP-Seq was combined with transcriptome analysis to identify global direct target genes of JAG. Consistent with the roles of JAG during organ initiation and organ growth, I found that JAG directly repressed genes involved in meristem development, such as the TALE PROTEIN BELL1 and genes involved in organ boundaries specification such as PETAL LOSS. In addition, JAG directly regulated genes involved in growth regulatory pathways, tissue polarity, cell wall modification, and cell cycle progression. For example, JAG directly repressed the cell cycle inhibitors KIP RELATED PROTEIN 2 and 4 (KRP2/4). The krp2 and krp4 mutations suppressed jag loss of function defects in organ growth and cell type patterning. In particular, loss of KRP4 rescued the defects of cell size homeostasis in the primordia of the jag loss of function mutant. In summary, this work revealed that JAG directly coordinates organ patterning with cellular processes required for tissue growth

An approach to modelling and describing software evolution processes

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Studies of lung function

This thesis outlines the candidate's contribution to the study of Respiratory Physiology in two main areas 1. The effect of lung morphometry on lung function and 2. Reflex control of pattern of breathing.The work that makes up this thesis is laid out in largely chronological order describing the evolution of the investigations.The effect of bronchial tree structure on function was investigated using a number of new techniques developed by the author. These include a method of modelling the bronchial tree to previously unobtained detail in the form of a hollow cast. This enabled gas transit times to airways of 2-3 mm diameter to be measured and the contribution made by architecture, tissue compliance and the gradient of pleural pressure to the distribution of ventilation to be apportioned. This was the first time transit times to individual airways had been measured. Using these techniques the effect of bronchial tree structure on the phenomenon of separation of gas mixtures into their components during breathing, and the effect of the beating heart on the mixing of gases during breathing was quantified. The author's contributions to the investigation of neural control of breathing follow. A fortuitous observation that SO₂ blocks pulmonary stretch receptors (PSR) in rabbits, which took place while developing an animal model of bronchitis, lead to the observation of a non PSR mechanism determining inspiratory time (ti). Investigation of the action of rapidly adapting pulmonary receptors (RAR) using SO₂ confirmed their role in provoking sighs or augmented breaths and demonstrated that they terminated expiratory duration (tn) with a constant latency. A consistent effect of RARs on inspiration proved elusive until it was discovered that after provoking an augmented breath ft is refractory to the direct effects of RAR activity for about 2 minutes. This observation lead to the development of a theoretical model of control of ft via a central linking. This explained our observation of a non-PSR effect restricting ft after SO₂ block. Further investigations confirmed a role for RAR in control of breathing in conscious dogs. The action of RAR in initiating inspiration was demonstrated using PSR block. The same technique was used to elucidate the role played by PSR in shifts in functional residual capacity during changes in posture. An interesting observation made at this time is that although cough is primarily associated with RAR activity it can not be triggered from the lungs. The results of experiments demonstrating a similar role for RAR in conscious animals are presented.The influence of high frequency ventilation, on pulmonary receptors, the reflexes they produce and on the non-Newtonian properties of bronchial mucus is described.The way in which different species control their very different frequencies of breathing is included and the way pulmonary receptor activity is changed in some models of lung disease. The effects of modern anaesthetics on receptor activity and the effect of acupuncture as a respiratory stimulant are reported. The results of some investigations of human movement and tremor are presented. The candidates contributions to books and books published are described

The Nottoway of Virginia: A Study of Peoplehood and Political Economy, c.1775-1875

This research examines the social construction of a Virginia Indian reservation community during the late eighteenth and nineteenth centuries. Between 1824 and 1877 the Iroquoian-speaking Nottoway divided their reservation lands into individual partible allotments and developed family farm ventures that mirrored their landholding White neighbors. In Southampton\u27s slave-based society, labor relationships with White landowners and Free People of Color impacted Nottoway exogamy and shaped community notions of peoplehood. Through property ownership and a variety of labor practices, Nottoway\u27s kin-based farms produced agricultural crops, orchard goods and hogs for export and sale in an emerging agro-industrial economy. However, shifts in Nottoway subsistence, land tenure and marriage practices undermined their matrilineal social organization, descent reckoning and community solidarity. With the asymmetrical processes of kin-group incorporation into a capitalist economy, questions emerge about the ways in which the Nottoway resituated themselves as a social group during the allotment process and after the devastation of the Civil War. Using an historical approach emphasizing world-systems theory, this dissertation investigates the transformation of the Nottoway community through an exploration and analysis of their nineteenth-century political economy and notions of peoplehood

The ILO @ 100

On the occasion of the centenary of the International Labour Organization (ILO), International Development Policy explores the Organization’s progress and gaps to date and its efforts to respond to the new challenges of the fourth industrial revolution, with regard to labour and social protection. Readership: Scholars, students, academic librarians and development practitioners interested in international organisations, the ILO, the future of work, working conditions, social protection, development policy, the 4th industrial revolution, rights and social justice, the green economy, reform, child labour, migrant labour, women’s labour, globalisation, automation, Asia, Africa, Europe and the informal economy