GAMS MINLP Solver comparisons and some improvements to the AlphaECP algorithm

I doktorsavhandlingen undersöks förmågan att lösa hos ett antal lösare för optimeringsproblem och ett antal svårigheter med att göra en rättvis lösarjämförelse avslöjas. Dessutom framläggs några förbättringar som utförts på en av lösarna som heter GAMS/AlphaECP. Optimering innebär, i det här sammanhanget, att finna den bästa möjliga lösningen på ett problem. Den undersökta klassen av problem kan karaktäriseras som svårlöst och förekommer inom ett flertal industriområden. Målet har varit att undersöka om det finns en lösare som är universellt snabbare och hittar lösningar med högre kvalitet än någon av de andra lösarna. Det kommersiella optimeringssystemet GAMS (General Algebraic Modeling System) och omfattande problembibliotek har använts för att jämföra lösare. Förbättringarna som presenterats har utförts på GAMS/AlphaECP lösaren som baserar sig på skärplansmetoden Extended Cutting Plane (ECP). ECP-metoden har utvecklats främst av professor Tapio Westerlund på Anläggnings- och systemteknik vid Åbo Akademi.

CFD Modelling of Direct Contact Condensation in Suppression Pools by Applying Condensation Models of Separated Flow

The condensation rate has to be high in the safety pressure suppression pool systems of Boiling Water Reactors (BWR) in order to fulfill their safety function. The phenomena due to such a high direct contact condensation (DCC) rate turn out to be very challenging to be analysed either with experiments or numerical simulations. In this thesis, the suppression pool experiments carried out in the POOLEX facility of Lappeenranta University of Technology were simulated. Two different condensation modes were modelled by using the 2-phase CFD codes NEPTUNE CFD and TransAT. The DCC models applied were the typical ones to be used for separated flows in channels, and their applicability to the rapidly condensing flow in the condensation pool context had not been tested earlier. A low Reynolds number case was the first to be simulated. The POOLEX experiment STB-31 was operated near the conditions between the ’quasi-steady oscillatory interface condensation’ mode and the ’condensation within the blowdown pipe’ mode. The condensation models of Lakehal et al. and Coste & Lavi´eville predicted the condensation rate quite accurately, while the other tested ones overestimated it. It was possible to get the direct phase change solution to settle near to the measured values, but a very high resolution of calculation grid was needed. Secondly, a high Reynolds number case corresponding to the ’chugging’ mode was simulated. The POOLEX experiment STB-28 was chosen, because various standard and highspeed video samples of bubbles were recorded during it. In order to extract numerical information from the video material, a pattern recognition procedure was programmed. The bubble size distributions and the frequencies of chugging were calculated with this procedure. With the statistical data of the bubble sizes and temporal data of the bubble/jet appearance, it was possible to compare the condensation rates between the experiment and the CFD simulations. In the chugging simulations, a spherically curvilinear calculation grid at the blowdown pipe exit improved the convergence and decreased the required cell count. The compressible flow solver with complete steam-tables was beneficial for the numerical success of the simulations. The Hughes-Duffey model and, to some extent, the Coste & Lavi´eville model produced realistic chugging behavior. The initial level of the steam/water interface was an important factor to determine the initiation of the chugging. If the interface was initialized with a water level high enough inside the blowdown pipe, the vigorous penetration of a water plug into the pool created a turbulent wake which invoked the chugging that was self-sustaining. A 3D simulation with a suitable DCC model produced qualitatively very realistic shapes of the chugging bubbles and jets. The comparative FFT analysis of the bubble size data and the pool bottom pressure data gave useful information to distinguish the eigenmodes of chugging, bubbling, and pool structure oscillations.

Cognitive Development of Very Low Birth Weight Children from Infancy to Pre-school Age

The survival of preterm born infants has increased but the prevalence of long-term morbidities has still remained high. Preterm born children are at an increased risk for various developmental impairments including both severe neurological deficits as well as deficits in cognitive development. According to the literature the developmental outcome perspective differs between countries, centers, and eras. Definitions of preterm infant vary between studies, and the follow-up has been carried out with diverse methods making the comparison less reliable. It is essential to offer parents upto-date information about the outcome of preterm infants born in the same area. A centralized follow-up of children at risk makes it possible to monitor the consequences of changes in the treatment practices of hospitals on developmental outcome. This thesis is part of a larger regional, prospective multidisciplinary follow-up project entitled “Development and Functioning of Very Low Birth Weight Infants from Infancy to School Age” (PIeniPAinoisten RIskilasten käyttäytyminen ja toimintakyky imeväisiästä kouluikään, PIPARI). The thesis consists of four original studies that present data of very low birth weight (VLBW) infants born between 2001 and 2006, who are followed up from the neonatal period until the age of five years. The main outcome measure was cognitive development and secondary outcomes were significant neurological deficits (cerebral palsy, CP, deafness, and blindness). In Study I, the early crying and fussing behavior of preterm infants was studied using parental diaries, and the relation of crying behavior and cognitive and motor development at the age of two years was assessed. In Study II, the developmental outcome (cognitive, CP, deafness, and blindness) at the age of two years was studied in relation to demographic, antenatal, neonatal, and brain imaging data. Development was studied in relationship to a full-term born control group born in the same hospital. In Study III, the stability of cognitive development was studied in VLBW and full-term groups by comparing the outcomes at the ages of two and five years. Finally, in Study IV the precursors of reading skills (phonological processing, rapid automatized naming, and letter knowledge) were assessed for VLBW and full-term children at the age of five years. Pre-reading skills were studied in relation to demographic, antenatal, neonatal, and brain imaging data. The main findings of the thesis were that VLBW infants who fussed or cried more in the infancy were not at greater risk for problems in their cognitive development. However, crying was associated with poorer motor development. The developmental outcome of the present population was better that has been reported earlier and this improvement covered also cognitive development. However, the difference to fullterm born peers was still significant. Major brain pathology and intestinal perforation were independent significant risk factors for adverse outcome, also when several individual risk factors were controlled for. Cognitive development at the age of two years was strongly related with development at the age of five years, stressing the importance of the early assessment, and the possibility for early interventions. Finally, VLBW children had poorer pre-reading skills compared with their full-term born peers, but the IQ was an important mediator even when children with mental retardation were excluded from the analysis. The findings suggest that counseling parents about the developmental perspectives of their preterm infant should be based on data covering the same birth hospital. Neonatal brain imaging data and neonatal morbidity are important predictors for developmental outcome. The findings of the present study stress the importance of both short-term (two years) and long-term (five years) follow-ups for the individual, and for improving the quality of care.

The spindle assembly checkpoint as a drug target - Novel small-molecule inhibitors of Aurora kinases

Cell division (mitosis) is a fundamental process in the life cycle of a cell. Equal distribution of chromosomes between the daughter cells is essential for the viability and well-being of an organism: loss of fidelity of cell division is a contributing factor in human cancer and also gives rise to miscarriages and genetic birth defects. For maintaining the proper chromosome number, a cell must carefully monitor cell division in order to detect and correct mistakes before they are translated into chromosomal imbalance. For this purpose an evolutionarily conserved mechanism termed the spindle assembly checkpoint (SAC) has evolved. The SAC comprises a complex network of proteins that relay and amplify mitosis-regulating signals created by assemblages called kinetochores (KTs). Importantly, minor defects in SAC signaling can cause loss or gain of individual chromosomes (aneuploidy) which promotes tumorigenesis while complete failure of SAC results in cell death. The latter event has raised interest in discovery of low molecular weight (LMW) compounds targeting the SAC that could be developed into new anti-cancer therapeutics. In this study, we performed a cell-based, phenotypic high-throughput screen (HTS) to identify novel LMW compounds that inhibit SAC function and result in loss of cancer cell viability. Altogether, we screened 65 000 compounds and identified eight that forced the cells prematurely out of mitosis. The flavonoids fisetin and eupatorin, as well as the synthetic compounds termed SACi2 and SACi4, were characterized in more detail utilizing versatile cell-based and biochemical assays. To identify the molecular targets of these SAC-suppressing compounds, we investigated the conditions in which SAC activity became abrogated. Eupatorin, SACi2 and SACi4 preferentially abolished the tensionsensitive arm of the SAC, whereas fisetin lowered also the SAC activity evoked by lack of attachments between microtubules (MTs) and KTs. Consistent with the abrogation of SAC in response to low tension, our data indicate that all four compounds inhibited the activity of Aurora B kinase. This essential mitotic protein is required for correction of erratic MT-KT attachments, normal SAC signaling and execution of cytokinesis. Furthermore, eupatorin, SACi2 and SACi4 also inhibited Aurora A kinase that controls the centrosome maturation and separation and formation of the mitotic spindle apparatus. In line with the established profound mitotic roles of Aurora kinases, these small compounds perturbed SAC function, caused spindle abnormalities, such as multi- and monopolarity and fragmentation of centrosomes, and resulted in polyploidy due to defects in cytokinesis. Moreover, the compounds dramatically reduced viability of cancer cells. Taken together, using a cell-based HTS we were able to identify new LMW compounds targeting the SAC. We demonstrated for the first time a novel function for flavonoids as cellular inhibitors of Aurora kinases. Collectively, our data support the concept that loss of mitotic fidelity due to a non-functional SAC can reduce the viability of cancer cells, a phenomenon that may possess therapeutic value and fuel development of new anti-cancer drugs.

Studies of Solar Activity with Emphasis on Quasi-Periodic Oscillations

In this thesis mainly long quasi-periodic solar oscillations in various solar atmospheric structures are discussed, based on data obtained at several wavelengths, focussing, however, mainly on radio frequencies. Sunspot (Articles II and III) and quiet Sun area (QSA) (Article I) oscillations are investigated along with quasi-periodic pulsations (QPP) in a flaring event with wide-range radio spectra (Article IV). Various oscillation periods are detected; 3–15, 35–70 and 90 minutes (QSA), 10-60 and 80-130 minutes (in sunspots at various radio frequencies), 3-5, 10-23, 220-240, 340 and 470 minutes (in sunspots at photosphere) and 8-12 and 15-17 seconds (in a solar flare at radio frequencies). Some of the oscillation periods are detected for the first time, while some of them have been confirmed earlier by other research groups. Solar oscillations can provide more information on the nature of various solar structures. This thesis presents the physical mechanisms of some solar structure oscillations. Two different theoretical approaches are chosen; magnetohydrodynamics (MHD) and the shallow sunspot model. These two theories can explain a wide range of solar oscillations from a few seconds up to some hours. Various wave modes in loop structures cause solar oscillations (<45 minutes) both in sunspots and quiet Sun areas. Periods lasting more than 45 minutes in the sunspots (and a fraction of the shorter periods) are related to sunspot oscillations as a whole. Sometimes similar oscillation periods are detected both in sunspot area variations and respectively in magnetic field strength changes. This result supports a concept that these oscillations are related to sunspot oscillations as a whole. In addition, a theory behind QPPs at radio frequencies in solar flares is presented. The thesis also covers solar instrumentation and data sources. Additionally, the data processing methods are presented. As the majority of the investigations in this thesis focus on radio frequencies, also the most typical radio emission mechanisms are presented. The main structures of the Sun, which are related to solar oscillations, are also presented. Two separate projects are included in this thesis. Solar cyclicity is studied using the extensively large solar radio map archieve from Metsähovi Radio Observatory (MRO) at 37 GHz, between 1978 and 2011 (Article V) covering two full solar cycles. Also, some new solar instrumentation (Article VI) was developed during this thesis.

Memoria virtualis - death and mourning rituals in online environments

The main objective of this work has been to understand the ritual aspect of how private people use the Internet to mourn and honor their intimates in various online environments. The research material was compiled in 2007–2013 through ethnographic and autoethnographic observations in social media applications, online memorial websites, one shared virtual environment (Second Life) and one massive multi-player online role-playing game (World of Warcraft). The research material consists of – in addition to the ethnographic observations – three online surveys with 153 respondents (mainly from Finland, the United States and the United Kingdom). In addition, the researcher conducted 38 longer online interviews (i.e. via email, an avatar). The theoretical framework is derived from ritual theory, hermeneutic-phenomenological anthropology and discourse analysis. The research questions are as follows: Why are death rituals practiced in online environments? How are virtual memorials created in various online environments? What kind of systems of meanings are virtual memorials constructed from? The results indicate that online mourning and honoring is appropriated in addition to the “traditional” offline rituals. In online environments the bereaved can choose, where, when, how and with whom they share their grief and loss. Memorials are created in the web intentionally and unintentionally, where the latter refers inter alia to the Facebook profile of the deceased where his/her intimates gather to mourn and honor immediately after the death. The first refers to intentionally memorialized online places spaces via different service providers. Virtual memorials are a way to construct the identity of the deceased, as well as the bereaved in multiple ways. They also re-enforce and create a sense of communality both privately and publicly, and enable one meaningful online place where all the intimates of the deceased can gather together to mourn and honor despite the geographical or time distances. Tämä väitöstutkimus tarkastelee miten nykyiset kuolemanrituaalit ovat digitalisoituneet verkkoympäristöihin. Tutkimus on suoritettu verkkoetnografisin sekä autoetnografisin menetelmin sosiaalisen median sivustoilla, virtuaalimuistomerkkipalveluissa, yhdestä virtuaalimaailmassa (Second Life) sekä yhdestä reaaliaikaisessa verkkopelissä (World of Warcraft) vuosina 2007–2013. Tutkimusaineisto koostuu etnografisten havainnointien lisäksi kolmesta verkkokyselystä, joissa vastaajia on yhteensä 153 pääasiassa Suomesta, Yhdysvalloista sekä Iso-Britanniasta. Kyselyjen lisäksi tutkija on tehnyt myös 38 laajempaa verkkohaastattelua eri ympäristöissä (esim. sähköposti, avatar virtuaalimaailmassa). Teoreettinen kehys koostuu rituaaliteoriasta, hermeneuttis-phenomenologiasta sekä diskurssianalyysista. Tutkimuskysymykset ovat seuraavat: miksi kuolemanrituaaleja harjoitetaan verkkoympäristöissä, miten virtuaalisia muistomerkkejä luodaan verkkoon, sekä millaisista merkitysjärjestelmistä virtuaaliset muistomerkit muodostuvat? Tutkimustulosten mukaan verkkosureminen ja muistaminen ovat tulleet perinteisten kuolemanrituaalien rinnalle, jolloin sureva itse voi päättää miten, missä, milloin sekä kenen kanssa suree läheistään. Muistomerkkejä verkkoon luodaan suunnitellusti (intentional) sekä suunnittelemattomasti (unintentional), jolloin jälkimmäinen viittaa esimerkiksi edesmenneen Facebook profiiliin, missä hänen läheisensä kokoontuvat muistelemaan ja suremaan välittömästi kuoleman jälkeen. Ensimmäinen taas viittaa suunnitelmalliseen muistomerkin luomiseen, jota varten löytyy useita palveluntarjoajia. Virtuaalimuistomerkit ovat keino rakentaa sekä edesmenneen että surevan identiteettiä, vahvistaa ja luoda yhteisöllisyyttä niin yksityisesti kuin julkisesti, sekä luoda yksi yhteinen aina ja kaikkialta saavutettavissa oleva merkityksellinen paikka verkkoon, missä kaikki läheiset voivat ajasta ja paikasta riippumatta muistella ja surra läheistään.

Paul and death : a study in psychological coping

The present investigation looks into the attitudes toward death in Paul’s authentic letters, and puts them in relation to modern theories of psychological coping. Drawing on psychologically-oriented hermeneutic theory, and theories about psychological coping in particular, I argue that each case of psychological coping must be understood in its historical situation as strategies emanating from a specific person’s subjective appraisal (cf. Pargament, Lazarus and Folkman). Paul’s letters frequently refer to persecution and violent death. To aid in psychological coping is often integral to the purpose of the letters, which makes the perspective of psychological coping akin to their genre. In the course of a tentatively assumed chronological order of 1 Thessalonians, Galatians, 1 Corinthians, 2 Corinthians, Romans, Philippians, and Philemon, Paul moves from the perception of Jesus dying for the faithful to the understanding of dying with Jesus. His coping strategies concerning death are gradually transformed from conservative and deferring coping styles, to a more self-directing coping style, to collaborative and transformative coping styles, and finally to a new sense of deferring coping style in prison. The last case of deferring coping carries the traits of generosity and flexibility even in the face of death, which is in contrast to his previous letters. Through his correspondence, we see Paul’s attitude toward death transformed from denial to reaction, to processing, to acceptance (cf. Lindemann, Kübler-Ross, Bowlby, Parkes, among others). His strategies also shift in accordance with these understandings. Denial is accompanied by diversion, threat by aggression, processing by rumination, and acceptance by joy. The study shows the hermeneutic benefits of reading Paul’s letters as the rhetorically framed expressions of a person in a particular historical situation. The letters open small windows through which we can glimpse the coping process of a person of antiquity. In adopting the method of psychological exegesis, the study shows that the variety of attitudes toward death in Paul’s letters makes sense from the perspective of psychological coping. The psychological aspect of these letters is an underexamined richness that can extend into areas of contemporary individual and group identity, and from there to public policy and ethics.

De obligationibus ex contractu vel quasi contractu

Arkit: A-B8.

Psychological well-being of the parents and child development, behavior, and quality of life in very low birth weight infants

The parents of premature infants, especially the mothers, are at increased risk for distress. Infants born prematurely are at risk for developmental problems. The aim of this study was to investigate whether the psychological well-being of both parents is associated with child development in very low birth weight (VLBW, ≤1500g) children. The burden of prematurity-related morbidity to the children and to the family was also assessed. A cohort of 201 VLBW infants born during 2001–2006 in the Turku University Hospital, Finland, and their parents were studied (I–IV). One study included a control group (n=166) of full-term infants (IV). The psychological well-being of the parents was evaluated by assessments of depressive symptoms, parenting stress, the sense of coherence and general family functioning. Cognitive, behavioral, and socio-emotional development, and the health-related quality of life (HRQoL) of the children were determined when the children were 2 to 8 years old. The psychological well-being of the parents was associated with the cognitive, behavioral and social development of the VLBW children. The VLBW infants with prematurity-related morbidities had a poorer HRQoL and the general functioning of the family was inferior compared to the control children and their families. 64.5% of the VLBW children survived without morbidities. Most of the VLBW children did not have significant behavior problems (93%), had normal social skills (63%), had no emotional problems (64%), and had no problems in executive functioning (62%). Only 3% of the surviving VLBW infants had significant cognitive delay. In conclusion, the depressive symptoms and stress of the parents can be risk factors for disadvantageous child development, while a strong sense of coherence can be protective. Parents of the premature children with developmental delays might also experience more depressive symptoms and stress than other parents. Prematurity-related morbidities were a burden to the VLBW child as well as to the family.