Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura

Gene flow (defined as allele exchange between populations) and gene flux (defined as allele exchange during meiosis in heterokaryotypic females) are important factors decreasing genetic differentiation between populations and inversions. Many chromosomal inversions are under strong selection and their role in recombination reduction enhances the maintenance of their genetic distinctness. Here we analyze levels and patterns of nucleotide diversity, selection and demographic history, using 37 individuals of Drosophila subobscura from Mount Parnes (Greece) and Barcelona (Spain). Our sampling focused on two frequent O-chromosome arrangements that differ by two overlapping inversions (OST and O3+4), which are differentially adapted to the environment as observed by their opposing latitudinal clines in inversion frequencies. The six analyzed genes (Pif1A, Abi, Sqd, Yrt, Atpa and Fmr1) were selected for their location across the O-chromosome and their implication in thermal adaptation. Despite the extensive gene flux detected outside the inverted region, significant genetic differentiation between both arrangements was found inside it. However, high levels of gene flow were detected for all six genes when comparing the same arrangement among populations. These results suggest that the adaptive value of inversions is maintained, regardless of the lack of genetic differentiation within arrangements from different populations, and thus favors the Local Adaptation hypothesis over the Coadapted Genome hypothesis as the basis of the selection acting on inversions in these populations.

Analysis of flow dynamics in right ventricular outflow tract.

BACKGROUND: The mechanism behind early graft failure after right ventricular outflow tract (RVOT) reconstruction is not fully understood. Our aim was to establish a three-dimensional computational fluid dynamics (CFD) model of RVOT to investigate the hemodynamic conditions that may trigger the development of intimal hyperplasia and arteriosclerosis. METHODS: Pressure, flow, and diameter at the RVOT, pulmonary artery (PA), bifurcation of the PA, and left and right PAs were measured in 10 normal pigs with a mean weight of 24.8 ± 0.78 kg. Data obtained from the experimental scenario were used for CFD simulation of pressure, flow, and shear stress profile from the RVOT to the left and right PAs. RESULTS: Using experimental data, a CFD model was obtained for 2.0 and 2.5-L/min pulsatile inflow profiles. In both velocity profiles, time and space averaged in the low-shear stress profile range from 0-6.0 Pa at the pulmonary trunk, its bifurcation, and at the openings of both PAs. These low-shear stress areas were accompanied to high-pressure regions 14.0-20.0 mm Hg (1866.2-2666 Pa). Flow analysis revealed a turbulent flow at the PA bifurcation and ostia of both PAs. CONCLUSIONS: Identified local low-shear stress, high pressure, and turbulent flow correspond to a well-defined trigger pattern for the development of intimal hyperplasia and arteriosclerosis. As such, this real-time three-dimensional CFD model may in the future serve as a tool for the planning of RVOT reconstruction, its analysis, and prediction of outcome.

Order-flow Standardization with Product Data Management Ideology

Tämän diplomityön päämääränä oli kuvata tilaus-toimitusprosessin eri toimintojen työnkulku, kun tuotetiedonhallintajärjestelmä on osa työympäristöä. Työn teoreettisessa osassa tarkasteltiin liiketoimintaprosessien uudistamista ja prosessien määrittämistä sekä esiteltiin tuotetiedonhallinnan (PDM) keskeiset osa-alueet. Kohdeyrityksen tausta ja strategiat esiteltiin, minkä jälkeen muutoksia arvioitiin suhteessa teoriaosuuden tuloksiin. Nykyisten toimintatapojen määrittämistä varten haastateltiin henkilöitä jokaisesta tilaus-toimitusprosessin vaiheesta tuotantoyksikön sisällä. Lopuksi kuvattiin yrityksen tuotetiedonhallintaperiaatteet ja määritettiin työnkulku prosessin eri vaiheissa. Samalla kuin uusi tuotetiedonhallintajärjestelmä otetaan käyttöön, on yrityksessä omaksuttava tuotetiedonhallinnan ajatusmalli. Tuoterakenteen hallinta jakautuu nyt eri toimintojen kesken, jolloin suunnittelun rakenne, tuotannon rakenne ja huoltorakenne ovat eri ihmisten vastuulla. Näiden eri rakenteiden konfigurointi tilaus-toimitus prosessin aikana määrää missä järjestyksessä toiminnot on suoritettava eri järjestelmien välillä. Monikansallinen suunnitteluorganisaatio on myös otettava huomioon tilauksenkulun aikana. Tuotetiedonhallintajärjestelmää käytetään yhdessä tuttujen suunnitteluohjelmien sekä toiminnanohjausjärjestelmän (ERP) kanssa. Työnkulkukaaviossa määritellään koko yritystä koskeva malli siitä, miten ja missä järjestyksessä tehtävät on suoritettava eri järjestelmissä tilaus-toimitus prosessin aikana. Tässä työssä tutkittiin tuotteen määrittelyn ja suunnittelutiedon hallinnan kannalta oleellisimmat tilaus-toimitusprosessiin kuuluvat toiminnot; myynti, myynnin tuki, tuotannon ohjaus, sovellussuunnittelu ja dokumentointi. Tulevaisuudessa on suositeltavaa pohtia tuotetiedonhallintajärjestelmän käyttöönottoa myös tuotannossa ja ostoissa. Tilaus-toimitusprosessiin liittyvät kehitysmahdollisuudet kannattaisi seuraavaksi kohdistaa tilauksen määrittelyvaiheeseen myyjä-asiakas rajapinnassa, jossa tehdyt virheet kertautuvat jokaisessa prosessin vaiheessa.

Stock flow through a drum screen

Tässä diplomityössä haluttiin mallintaa kuidutusrummun toimintaa Fluent virtausmallinusohjelman avulla. Aikaisempi tieto ja kehitystyö on perustunut kokemukseen ja käytännön kokeisiin. Kehitystyön alkuaikoina on suoritettu muutamia laskelmia koskien rummun tuottoa mutta sen jälkeen ei toimintaa ole laskennallisesti kuvattu. Työn ensimmäinen osa käsittelee yleisesti keräyspaperin käsittelyyn liittyviä laitteita ja menetelmiä. Toimintaperiaatteita on kuvattu yleisellä tasolla ja FibreFlow® rumpu on sitten käsitelty muita laitteita tarkemmin. Työn toinen osa sisältää sitten laboratoriotestit paikallisilta tahteilta hankittujen näytteiden viskositeettien ja tiheyksien määrittämiseksi. Kokeet suoritettiin Kemiantekniikan osastolla Brookfield viskoosimetrillä. Joitain alustavia laskentoja tuotosta suoritettiin aikaisempien tietojen perusteella. Rumpua kun on valmistettu vuodesta 1976, on tietoa kertynyt runsaasti vuosien mittaan. Laskelmia varten valittiin mallinnettavaksi alueeksi vain yksittäinen reikä sihdistä jolle laskettiin massavirta. Käytetyt laadut olivat OCC ja DIP. Myös eri rumpukoot otettiin jossain määrin huomioon.

Fluid dynamical prediction of changed v1-flow at energies available at the CERN Large Hadron Collider

Substantial collective flow is observed in collisions between lead nuclei at Large Hadron Collider (LHC) as evidenced by the azimuthal correlations in the transverse momentum distributions of the produced particles. Our calculations indicate that the global v1-flow, which at RHIC peaked at negative rapidities (named third flow component or antiflow), now at LHC is going to turn toward forward rapidities (to the same side and direction as the projectile residue). Potentially this can provide a sensitive barometer to estimate the pressure and transport properties of the quark-gluon plasma. Our calculations also take into account the initial state center-of-mass rapidity fluctuations, and demonstrate that these are crucial for v1 simulations. In order to better study the transverse momentum flow dependence we suggest a new"symmetrized" vS1(pt) function, and we also propose a new method to disentangle global v1 flow from the contribution generated by the random fluctuations in the initial state. This will enhance the possibilities of studying the collective Global v1 flow both at the STAR Beam Energy Scan program and at LHC.

Optimizing nozzle flow in laser cutting

The purpose of this study was to investigate different laser cutting nozzles, nozzle flows and possibilities to improve nozzle flow. Another goal was to design new nozzle configuration in which laser cutting would succeed with better cutting speed and smaller gas consumption. Nozzles and nozzle flows were studied with various methods. Computational fluid dynamics was used to calculate old, convergent nozzles and new convergent-divergent nozzles. Measurement apparatus was used to measure both nozzle types. In cutting tests different materials were cut with new nozzles. With the use of design convergent-divergent nozzles 25 % better cutting speed and 33 % smaller gas consumption were achieved when cutting quality was good. Computational fluid dynamics was also discovered to be useful aid in nozzle design.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.

Pain-evoked alterations on gingival blood flow and gingival crevicular fluid (GCF) neuropeptide SP and collagenase-2 (MMP-8) levels

Previous studies have demonstrated that clinical pulpal pain can induce the expression of pro-inflammatory neuropeptides in the adjacent gingival crevice fluid (GCF). Vasoactive agents such as substance P (SP) are known to contribute to the inflammatory type of pain and are associated with increased blood flow. More recent animal studies have shown that application of capsaicin on alveolar mucosa provokes pain and neurogenic vasodilatation in the adjacent gingiva. Pain-associated inflammatory reactions may initiate expression of several pro- and anti-inflammatory mediators. Collagenase-2 (MMP-8) has been considered to be the major destructive protease, especially in the periodontitis-affected gingival crevice fluid (GCF). MMP-8 originates mostly from neutrophil leukocytes, the first line of defence cells that exist abundantly in GCF, especially in inflammation. With this background, we wished to clarify the spatial extensions and differences between tooth-pain stimulation and capsaicin-induced neurogenic vasodilatation in human gingiva. Experiments were carried out to study whether tooth stimulation and capsaicin stimulation of alveolar mucosa would induce changes in GCF MMP-8 levels and whether tooth stimulation would release neuropeptide SP in GCF. The experiments were carried out on healthy human volunteers. During the experiments, moderate and high intensity painful tooth stimulation was performed by a constant current tooth stimulator. Moderate tooth stimulation activates A-delta fibres, while high stimulation also activates C-fibres. Painful stimulation of the gingiva was achieved by topical application of capsaicin-moistened filter paper on the mucosal surface. Capsaicin is known to activate selectively nociceptive C-fibres of stimulated tissue. Pain-evoked vasoactive changes in gingivomucosal tissues were mapped by laser Doppler imaging (LDI), which is a sophisticated and non-invasive method for studying e.g. spatial and temporal characteristics of pain- and inflammation-evoked blood flow changes in gingivomucosal tissues. Pain-evoked release of MMP-8 in GCF samples was studied by immunofluorometric assay (IFMA) and Western immunoblotting. The SP levels in GCF were analysed by Enzyme immunoassay (EIA). During the experiments, subjective stimulus-evoked pain responses were determined by a visual analogue pain scale. Unilateral stimulation of alveolar mucosa and attached gingiva by capsaicin evoked a distinct neurogenic vasodilatation in the ipsilateral gingiva, which attenuated rapidly at the midline. Capsaicin stimulation of alveolar mucosa provoked clear inflammatory reactions. In contrast to capsaicin stimuli, tooth stimulation produced symmetrical vasodilatations bilaterally in the gingiva. The ipsilateral responses were significantly smaller during tooth stimulation than during capsaicin stimuli. The current finding – that tooth stimulation evokes bilateral vasodilatation while capsaicin stimulation of the gingiva mainly produces unilateral vasodilatation – emphasises the usefulness of LDI in clarifying spatial features of neurogenic vasoactive changes in the intra-oral tissues. Capsaicin stimulation of the alveolar mucosa induced significant elevations in MMP-8 levels and activation in GCF of the adjacent teeth. During the experiments, no marked changes occurred in MMP-8 levels in the GCF of distantly located teeth. Painful stimulation of the upper incisor provoked elevations in GCF MMP-8 and SP levels of the stimulated tooth. The GCF MMP-8 and SP levels of the non-stimulated teeth were not changed. These results suggest that capsaicin-induced inflammatory reactions in gingivomucosal tissues do not cross the midline in the anterior maxilla. The enhanced reaction found during stimulation of alveolar mucosa indicates that alveolar mucosa is more sensitive to chemical irritants than the attached gingiva. Analysis of these data suggests that capsaicin-evoked neurogenic inflammation in the gingiva can trigger the expression and activation of MMP-8 in GCF of the adjacent teeth. In this study, it is concluded that experimental tooth pain at C-fibre intensity can induce local elevations in MMP-8 and SP levels in GCF. Depending on the role of MMP-8 in inflammation, in addition to surrogated tissue destruction, the elevated MMP-8 in GCF may also reflect accelerated local defensive and anti-inflammatory reactions.

New method for measuring longitudinal fuctuations and directed flow in ultrarelativistic heavy ion reactions

It has been shown in recent ALICE@LHC measurements that the odd flow harmonics, in particular, a directed flow v1, occurred to be weak and dominated by random fluctuations. In this work we propose a new method, which makes the measurements more sensitive to the flow patterns showing global collective symmetries. We demonstrate how the longitudinal center of mass rapidity fluctuations can be identified, and then the collective flow analysis can be performed in the event-by-event center of mass frame. Such a method can be very effective in separating the flow patterns originating from random fluctuations, and the flow patterns originating from the global symmetry of the initial state.

Architectural characterization of a delta-front reservoir analogue combining ground penetrating radar and electrical resistivity tomography: Roda Sandstone (Lower Eocene, Graus-Tremp basin, Spain)

Three-dimensional reconstruction of reservoir analogues can be improved combining data from different geophysical methods. Ground Penetrating Radar (GPR) and Electrical Resistivity Tomography (ERT) data are valuable tools, since they provide subsurface information from internal architecture and facies distribution of sedimentary rock bodies, enabling the upgrading of depositional models and heterogeneity reconstruction. The Lower Eocene Roda Sandstone is a well-known deltaic complex widely studied as a reservoir analogue that displays a series of sandstone wedges with a general NE to SW progradational trend. To provide a better understanding of internal heterogeneity of a 10m-thick progradational delta-front sandstone unit, 3D GPR data were acquired. In addition, common midpoints (CMP) to measure the sandstone subsoil velocity, test profiles with different frequency antennas (25, 50 and 100MHz) and topographic data for subsequent correction in the geophysical data were also obtained. Three ERT profiles were also acquired to further constrain GPR analysis. These geophysical results illustrate the geometry of reservoir analogue heterogeneities both depositional and diagenetic in nature, improving and complementing previous outcrop-derived data. GPR interpretation using radar stratigraphy principles and attributes analysis provided: 1)tridimensional geometry of major stratigraphic surfaces that define four units in the GPR Prism, 2) image the internal architecture of the units and their statistical study of azimuth and dips, useful for a quick determination of paleocurrent directions. These results were used to define the depositional architecture of the progradational sandbody that shows an arrangement in very-high-frequency sequences characterized by clockwise paleocurrent variations and decrease of the sedimentary flow, similar to those observed at a greater scale in the same system. This high-frequency sequential arrangement has been attributed to the autocyclic dynamics of a supply-dominated delta- front where fluvial and tidal currents are in competition. The resistivity models enhanced the viewing of reservoir quality associated with cement distribution caused by depositional and early diagenetic processes related to the development of transgressive and regressive systems tracts in igh-frequency sequences.