Research resource: the dynamic transcriptional profile of sertoli cells during the progression of spermatogenesis.

Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility.

Tilastotietojen graafinen esittäminen WWW-sivulla

World Wide Webin suosiolla on ollut merkittävä vaikutus yhteiskuntaan. WWW-sivut ovat helposti saatavilla ja sisällön tekeminen WWW:hen on helppoa. WWW-ympäristölle myös kehitetään paljon sovelluksia. WWW-sovellusten kehittämiselle ominaista on valinnanvapaus ja nopeuden tavoittelu. WWW-sovellusten ohjelmoinnin mahdollistavat useat toisilleen vaihtoehtoiset tekniikat. Ne eroavat toisistaan suoritusnopeudessa, ominaisuuksien määrässä ja joustavuudessa. Ohjelmoinnissa käytetään apuna useita erilaisia menetelmiä. Apumenetelmiä ovat muun muassa työkalut ja valmiiden komponenttien hyödyntäminen. Valmiit komponentit voivat olla joko ilmaisia, avointa lähdekoodia tai maksullisia. Tämän kandidaatintyön aikana valmistui sovellus, joka piirtää tilastotiedoista kaaviokuvia ja näyttää niitä dynaamisella WWW-sivulla. Sovellus pyrittiin toteuttamaan älykkäästi apumenetelmiä sopivasti hyödyntäen. Sovelluksen kehittämisessä käytettiin apuna sekä ohjelmointityökaluja että valmiita komponentteja. Kaaviokuvien tyypin ja ulkoasun haluttiin olevan käyttäjien muokattavissa. Toisaalta sovelluksen haluttiin olevan helposti laajennettavissa. Vaatimuksiin vastattiin tekemällä kaaviokuvien piirrosta osittain tietokannalla ohjelmoitava.

Formalizing argumentative reasoning in a possibilistic logic programming setting with fuzzy unification

Possibilistic Defeasible Logic Programming (P-DeLP) is a logic programming language which combines features from argumentation theory and logic programming, incorporating the treatment of possibilistic uncertainty at the object-language level. In spite of its expressive power, an important limitation in P-DeLP is that imprecise, fuzzy information cannot be expressed in the object language. One interesting alternative for solving this limitation is the use of PGL+, a possibilistic logic over Gödel logic extended with fuzzy constants. Fuzzy constants in PGL+ allow expressing disjunctive information about the unknown value of a variable, in the sense of a magnitude, modelled as a (unary) predicate. The aim of this article is twofold: firstly, we formalize DePGL+, a possibilistic defeasible logic programming language that extends P-DeLP through the use of PGL+ in order to incorporate fuzzy constants and a fuzzy unification mechanism for them. Secondly, we propose a way to handle conflicting arguments in the context of the extended framework.

A logic programming framework for possibilistic argumentation: formalization and logical properties

In the last decade defeasible argumentation frameworks have evolved to become a sound setting to formalize commonsense, qualitative reasoning. The logic programming paradigm has shown to be particularly useful for developing different argument-based frameworks on the basis of different variants of logic programming which incorporate defeasible rules. Most of such frameworks, however, are unable to deal with explicit uncertainty, nor with vague knowledge, as defeasibility is directly encoded in the object language. This paper presents Possibilistic Logic Programming (P-DeLP), a new logic programming language which combines features from argumentation theory and logic programming, incorporating as well the treatment of possibilistic uncertainty. Such features are formalized on the basis of PGL, a possibilistic logic based on G¨odel fuzzy logic. One of the applications of P-DeLP is providing an intelligent agent with non-monotonic, argumentative inference capabilities. In this paper we also provide a better understanding of such capabilities by defining two non-monotonic operators which model the expansion of a given program P by adding new weighed facts associated with argument conclusions and warranted literals, respectively. Different logical properties for the proposed operators are studied

Fire management, climate change and their interacting effects on birds in complex Mediterranean landscapes: dynamic distribution modelling of an early-successional species - the near-threatened Dartford Warbler (Sylvia undata)

The current challenge in a context of major environmental changes is to anticipate the responses of species to future landscape and climate scenarios. In the Mediterranean basin, climate change is one the most powerful driving forces of fire dynamics, with fire frequency and impact having markedly increased in recent years. Species distribution modelling plays a fundamental role in this challenge, but better integration of available ecological knowledge is needed to adequately guide conservation efforts. Here, we quantified changes in habitat suitability of an early-succession bird in Catalonia, the Dartford Warbler (Sylvia undata) ― globally evaluated as Near Threatened in the IUCN Red List. We assessed potential changes in species distributions between 2000 and 2050 under different fire management and climate change scenarios and described landscape dynamics using a spatially-explicit fire-succession model that simulates fire impacts in the landscape and post-fire regeneration (MEDFIRE model). Dartford Warbler occurrence data were acquired at two different spatial scales from: 1) the Atlas of European Breeding Birds (EBCC) and 2) Catalan Breeding Bird Atlas (CBBA). Habitat suitability was modelled using five widely-used modelling techniques in an ensemble forecasting framework. Our results indicated considerable habitat suitability losses (ranging between 47% and 57% in baseline scenarios), which were modulated to a large extent by fire regime changes derived from fire management policies and climate changes. Such result highlighted the need for taking the spatial interaction between climate changes, fire-mediated landscape dynamics and fire management policies into account for coherently anticipating habitat suitability changes of early succession bird species. We conclude that fire management programs need to be integrated into conservation plans to effectively preserve sparsely forested and early succession habitats and their associated species in the face of global environmental change.

Dynamic and quasistatic trajectories in quasifission reactions and particle emission

We show that the quasifission paths predicted by the one-body dissipation dynamics, in the slowest phase of a binary reaction, follow a quasistatic path, which represents a sequence of states of thermal equilibrium at a fixed value of the deformation coordinate. This establishes the use of the statistical particle-evaporation model in the case of dynamical time-evolving systems. Pre- and post-scission multiplicities of neutrons and total multiplicities of protons and α particles in fission reactions of 63Cu+92Mo, 60Ni+100Mo, 63Cu+100Mo at 10 MeV/u and 20Ne+144,148,154Sm at 20 MeV/u are reproduced reasonably well with statistical model calculations performed along dynamic trajectories whose slow stage (from the most compact configuration up to the point where the neck starts to develop) lasts some 35×10−21 s.

Web Services In Symbian OS

This thesis presents different aspects of Web Services usage in Symbian OS that is an operating system for handheld devices. The practical part of the work was to develop Symbian OS client application for Web Services. It produced four reusable software components. XML enables platform and programming language independent services. Web Services use XML to create standardized message oriented services that are accessed through HTTP. Web Services are moving towards dynamic B2B interaction. Web Services increases the amount of transferred data, which is not desirable in mobile networks where transfer speed is slower than in the traditional networks. However the modern mobile networks are able to transfer the extra payload with reasonable time. XML processing is not a big problem. Web Services can be accessed from the modern mobile devices and they can cut down the development costs.

Simulation Supported Robot Programming using XML

The main objective of this master's thesis is to study robot programming using simulation software, and also how to embed the simulation software into company's own robot controlling software. The further goal is to study a new communication interface to the assembly line's components -more precisely how to connect the robot cell into this new communication system. Conveyor lines are already available where the conveyors use the new communication standard. The robot cell is not yet capable of communicating with to other devices using the new communication protocols. The main problem among robot manufacturers is that they all have their own communication systems and programming languages. There has not been any common programming language to program all the different robot manufacturers robots, until the RRS (Realistic Robot Simulation) standards were developed. The RRS - II makes it possible to create the robot programs in the simulation software and it gives a common user interface for different robot manufacturers robots. This thesis will present the RRS - II standard and the robot manufacturers situation for the RRS - II support. Thesis presents how the simulation software can be embedded into company's own robot controlling software and also how the robot cell can be connected to the CAMX (Computer Aided Manufacturing using XML) communication system.

Dynamic Capabilities and Real Options

Tutkielman tavoitteena oli selvittää dynaamisten kyvykkyyksien teorian kehittymistä ja nykytilaa. Työssä tarkastellaan myös mahdollisuuksia yhdistää reaalioptioajattelua ja dynaamisten kyvykkyyksien teoriaa. Tutkielma on toteutettu teoreettisena kirjallisuuskatsauksena. Dynaamisten kyvykkyyksien teorian mukaan muuttuvassa toimintaympäristössä yritysten kilpailuetu perustuu kykyyn rakentaa, yhdistää ja muokata resursseja ja kyvykkyyksiä. Yritysten täytyy pystyä löytämään, sulauttamaan ja muuntamaan tietoa voidakseen tunnistaa uusia mahdollisuuksia ja pystyäkseen reagoimaan niihin. Tutkielma tuo esille uusia yhteyksiä dynaamisten kyvykkyyksien teorian ja yritysten käyttäytymisen välillä. Reaalioptioajattelu auttaa tunnistamaan yrityksen rajojen määrittämiseen vaikuttavia tekijöitä. Työssä tehdään ehdotuksia dynaamisten kyvykkyyksien teorian jatkotutkimusta varten.

Adaptive Protocol Stacks for Mobile Devices

Tulevaisuudessa siirrettävät laitteet, kuten matkapuhelimet ja kämmenmikrot, pystyvät muodostamaan verkkoyhteyden käyttäen erilaisia yhteysmenetelmiä eri tilanteissa. Yhteysmenetelmillä on toisistaan poikkeavat viestintäominaisuudet mm. latenssin, kaistanleveyden, virhemäärän yms. suhteen. Langattomille yhteysmenetelmille on myös ominaista tietoliikenneyhteyden ominaisuuksien voimakas muuttuminen ympäristön suhteen. Parhaan suorituskyvyn ja käytettävyyden saavuttamiseksi, on siirrettävän laitteen pystyttävä mukautumaan käytettyyn viestintämenetelmään ja viestintäympäristössä tapahtuviin muutoksiin. Olennainen osa tietoliikenteessä ovat protokollapinot, jotka mahdollistavat tietoliikenneyhteyden järjestelmien välillä tarjoten verkkopalveluita päätelaitteen käyttäjäsovelluksille. Jotta protokollapinot pystyisivät mukautumaan tietyn viestintäympäristön ominaisuuksiin, on protokollapinon käyttäytymistä pystyttävä muuttamaan ajonaikaisesti. Perinteisesti protokollapinot ovat kuitenkin rakennettu muuttumattomiksi niin, että mukautuminen tässä laajuudessa on erittäin vaikeaa toteuttaa, ellei jopa mahdotonta. Tämä diplomityö käsittelee mukautuvien protokollapinojen rakentamista käyttäen komponenttipohjaista ohjelmistokehystä joka mahdollistaa protokollapinojen ajonaikaisen muuttamisen. Toteuttamalla esimerkkijärjestelmän, ja mittaamalla sen suorituskykyä vaihtelevassa tietoliikenneympäristössä, osoitamme, että mukautuvat protokollapinot ovat mahdollisia rakentaa ja ne tarjoavat merkittäviä etuja erityisesti tulevaisuuden siirrettävissä laitteissa.

Dynamic Criteria: a Longitudinal Analysis of Professional Basketball Players" Outcomes

This paper describes the fluctuations of temporal criteria dynamics in the context of professional sport. Specifically, we try to verify the underlying deterministic patterns in the outcomes of professional basketball players. We use a longitudinal approach based on the analysis of the outcomes of 94 basketball players over ten years, covering practically players" entire career development. Time series were analyzed with techniques derived from nonlinear dynamical systems theory. These techniques analyze the underlying patterns in outcomes without previous shape assumptions (linear or nonlinear). These techniques are capable of detecting an intermediate situation between randomness and determinism, called chaos. So they are very useful for the study of dynamic criteria in organizations. We have found most players (88.30%) have a deterministic pattern in their outcomes, and most cases are chaotic (81.92%). Players with chaotic patterns have higher outcomes than players with linear patterns. Moreover, players with power forward and center positions achieve better results than other players. The high number of chaotic patterns found suggests caution when appraising individual outcomes, when coaches try to find the appropriate combination of players to design a competitive team, and other personnel decisions. Management efforts must be made to assume this uncertainty.

Dynamic arrest in polymer melts: competition between packing and intramolecular barriers

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within the framework of the mode coupling theory of the glass transition. Control parameters are tuned in order to induce a competition between general packing effects and polymer-specific intramolecular barriers as mechanisms for dynamic arrest. This competition yields unusually large values of the so-called mode coupling theory exponent parameter and rationalizes qualitatively different observations for simple bead-spring and realistic polymers. The systematic study of the effect of intramolecular barriers presented here also establishes a fundamental difference between the nature of the glass transition in polymers and in simple glass formers.

Dynamic single cell measurements of kinase activity by synthetic kinase activity relocation sensors.

BACKGROUND: Mitogen activated protein kinases (MAPK) play an essential role in integrating extra-cellular signals and intra-cellular cues to allow cells to grow, adapt to stresses, or undergo apoptosis. Budding yeast serves as a powerful system to understand the fundamental regulatory mechanisms that allow these pathways to combine multiple signals and deliver an appropriate response. To fully comprehend the variability and dynamics of these signaling cascades, dynamic and quantitative single cell measurements are required. Microscopy is an ideal technique to obtain these data; however, novel assays have to be developed to measure the activity of these cascades. RESULTS: We have generated fluorescent biosensors that allow the real-time measurement of kinase activity at the single cell level. Here, synthetic MAPK substrates were engineered to undergo nuclear-to-cytoplasmic relocation upon phosphorylation of a nuclear localization sequence. Combination of fluorescence microscopy and automated image analysis allows the quantification of the dynamics of kinase activity in hundreds of single cells. A large heterogeneity in the dynamics of MAPK activity between individual cells was measured. The variability in the mating pathway can be accounted for by differences in cell cycle stage, while, in the cell wall integrity pathway, the response to cell wall stress is independent of cell cycle stage. CONCLUSIONS: These synthetic kinase activity relocation sensors allow the quantification of kinase activity in live single cells. The modularity of the architecture of these reporters will allow their application in many other signaling cascades. These measurements will allow to uncover new dynamic behaviour that previously could not be observed in population level measurements.