Inferring stochastic regulatory networks from perturbations of the non-equilibrium steady state

Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A long-standing aim of quantitative biology is to reconstruct such networks on the basis of large-scale data. Our aim is to leverage fluctuations around the non-equilibrium steady state for network inference. To this end, we use a stochastic model of gene regulation or neural dynamics and solve it approximately within a Gaussian mean-field theory. We develop a likelihood estimate based on this stochastic theory to infer regulatory interactions from perturbation data on the network nodes. We apply this approach to artificial perturbation data as well as to phospho-proteomic data from cell-line experiments and compare our results to inference schemes restricted to mean activities in the steady state.Comment: 9 page

The Digital Constellation

The emergence of the digital society has become one of the most pressing research topics in social science. So far, political science has been at the margins of the debate because it has been restricted by a rather narrow focus on networked communications. The paper attempts to change this by presenting a more encompassing way to address digitalisation from within political science. After briefly criticising the development of the research in political science the paper reconstructs at length some of the most popular conceptualisations in neighbouring disciplines. While we highlight the commonalities and strengths of those approaches in theorising digitalisation, we criticise their rather derivative understanding of democratic practices and the political as such. We go on to propose a modified understanding - which we term the "digital constellation" - that looks at the changing shape of democracy by developing a much more nuanced understanding of the interplay between societies and technologies. Finally, we illustrate the argument in an exemplary analysis of the changes occurring in political representation in the context of digitalisation

Sequential Transfer Machine Learning in Networks: Measuring the Impact of Data and Neural Net Similarity on Transferability

In networks of independent entities that face similar predictive tasks, transfer machine learning enables to re-use and improve neural nets using distributed data sets without the exposure of raw data. As the number of data sets in business networks grows and not every neural net transfer is successful, indicators are needed for its impact on the target performance-its transferability. We perform an empirical study on a unique real-world use case comprised of sales data from six different restaurants. We train and transfer neural nets across these restaurant sales data and measure their transferability. Moreover, we calculate potential indicators for transferability based on divergences of data, data projections and a novel metric for neural net similarity. We obtain significant negative correlations between the transferability and the tested indicators. Our findings allow to choose the transfer path based on these indicators, which improves model performance whilst simultaneously requiring fewer model transfers

Ship emissions of SO2 and NO2: DOAS measurements from airborne platforms

A unique methodology to measure gas fluxes of SO2 and NO2 from ships using optical remote sensing is described and demonstrated in a feasibility study. The measurement system is based on Differential Optical Absorption Spectroscopy using reflected skylight from the water surface as light source. A grating spectrometer records spectra around 311 nm and 440 nm, respectively, with the telescope pointed downward at a 30A degrees angle from the horizon. The mass column values of SO2 and NO2 are retrieved from each spectrum and integrated across the plume. A simple geometric approximation is used to calculate the optical path. To obtain the total emission in kg h(-1) the resulting total mass across the plume is multiplied with the apparent wind, i.e. a dilution factor corresponding to the vector between the wind and the ship speed. The system was tested in two feasibility studies in the Baltic Sea and Kattegat, from a CASA-212 airplane in 2008 and in the North Sea outside Rotterdam from a Dauphin helicopter in an EU campaign in 2009. In the Baltic Sea the average SO2 emission out of 22 ships was (54 +/- 13) kg h(-1), and the average NO2 emission was (33 +/- 8) kg h(-1), out of 13 ships. In the North Sea the average SO2 emission out of 21 ships was (42 +/- 11) kg h(-1), NO2 was not measured here. The detection limit of the system made it possible to detect SO2 in the ship plumes in 60% of the measurements when the described method was used. A comparison exercise was carried out by conducting airborne optical measurements on a passenger ferry in parallel with onboard measurements. The comparison shows agreement of (-30 +/- 14)% and (-41 +/- 11)%, respectively, for two days, with equal measurement precision of about 20%. This gives an idea of the measurement uncertainty caused by errors in the simple geometric approximation for the optical light path neglecting scattering of the light in ocean waves and direct and multiple scattering in the exhaust plume under various conditions. A tentative error budget indicates uncertainties within 30-45% but for a reliable error analysis the optical light path needs to be modelled. A ship emission model, FMI-STEAM, has been compared to the optical measurements showing an 18% overestimation and a correlation coefficient (R-2) of 0.6. It is shown that a combination of the optical method with modelled power consumption can estimate the sulphur fuel content within 40%, which would be sufficient to detect the difference between ships running at 1% and at 0.1%, limits applicable within the IMO regulated areas

Solceller i elnät - Betydande andel solcellers inverkan på lågspänningsnätet

PV power production is becoming more and more common and one can easily imagine that a so called boom is near in southern Sweden. As the distribution grids are designed for power flow out to the households, and not the other way around, the question is what will happen that sunny day when the households in a neighborhood produce more electricity than they consume. This master thesis project was carried out at Lund University in collaboration with the local Distribution System Operator (DSO), Lunds Energi. It brings up the question of how a considerable amount of PV systems in the low-voltage grid affects power quality. This was made through simulations of three different model representations of existing low-voltage grids in Lund. Voltage variations, asymmetry and harmonics were the investigated power quality issues. The thesis was limited to PV systems of a size that can be expected to reach a larger incidence. The concluded guidelines should be applied to low-voltage grids similar to those modeled. The simulations have been made in DIgSILENT PowerFactory. The report also summerizes interviews with different Swedish DSOs and previous work reported in literature. Current regulations and standards were also reviewed. Results show that asymmetry is the most critical restriction, when a sufficient amount of single phase installations are unevenly distributed on the three phases throughout the grid. If all customers in a low-voltage grid install the amount of PV systems that their roofs allow, the voltage variations will only be unacceptable in the weakest points in the weakest grid. Voltage varations due to clouds passing the sun will not cause problems, based on the results from the simulations. Harmonics may form a potential danger to power quality, and depend on the quality of the inverters. The DSOs cannot deny an application for installation of a PV system that fulfill the requirements, and can only make sure that their grids can support the new installation. To this day, the amount of applications in Sweden is small enough for the DSO to investigate each one. But if a PV boom takes place with more than 100 applications per day on average, this is not realistic anymore. Therefore, a few simple guidelines are suggested to advise the DSOs, helping them recognize which applications that need extra consideration while unproblematic cases are approved without detailed investigation

Kapitalstruktur i familjeföretag - en studie av ägarstrukturens inverkan på kapitalstruktur

Syftet med denna uppsats är att med stöd av tre olika definitioner av familjeföretag, utreda om det föreligger systematiska skillnader mellan kapitalstrukturen i familjeföretag och icke-familjeföretag samt om förekomsten eller avsaknaden av sådana, kan förklaras av de teorier och tankegångar som presenteras i de praktiska- och teoretiska referensramarna. Uppsatsen har genomförts med hjälp av en kvantitativ studie och utgått ifrån ett deduktivt perspektiv. Information har inhämtats från årsredovisningar och med hjälp av denna har regressioner genomförts för varje familjevariabel. Resultatet visar att variablerna, storlek, tillväxt och andel materiella anläggningstillgångar påvisar signifikant samband på kapitalstruktur, medan familjeägande, utdelning och lönsamhet inte gör det. Slutsatsen är att agentteorier tillsammans med den praktiska referensramen skapar en komplex bild av familjeföretags incitamentsstruktur och dessutom bidrar problemen med att definiera familjebolag till ökad komplexitet. Sammantaget torde detta kunna förklara varför undersökningens resultat inte kunde påvisa några signifikanta skillnader mellan familjebolag och icke-familjebolag avseende skuldsättning

Die digitale Konstellation: eine Positionsbestimmung

Die Entwicklung der digitalen Gesellschaft ist in den Sozialwissenschaften zu einem zentralen Forschungsgegenstand aufgestiegen; in der Politikwissenschaft gilt allerdings, dass die Auseinandersetzung auf eher wenige Schwerpunkte - insbesondere Digitalisierung als vernetzte Kommunikation - beschränkt geblieben ist. Der Beitrag macht einen Vorschlag für eine andere Form der politikwissenschaftlichen Auseinandersetzung indem er - nach einer kritischen Rekonstruktion der Forschungsentwicklung in der Politikwissenschaft - breit rezipierte Diagnosen der digitalen Gesellschaft in Nachbardisziplinen wie der Soziologie und Rechtswissenschaft (Baecker, Nassehi, Reckwitz, Stalder und Vesting) rekonstruiert. Er arbeitet übergreifende Erkenntnisse im Digitalisierungsverständnis dieser Ansätze heraus, kritisiert jedoch deren Konzeptualisierung von Politik und Demokratie. Auf dieser Grundlage wird sodann ein Vorschlag unterbreitet, eine in der Politikwissenschaft anschlussfähigere Perspektive mittels des Konzepts der "digitalen Konstellation" zu entwickeln. Dieses untersucht das Wechselspiel technischer und gesellschaftlicher Entwicklungen in Bezug auf den Zusammenhang zum Formwandel von Demokratie. Abschließend wird dies in einer exemplarischen Analyse von Veränderungen des Repräsentationskonzepts im digitalen Kontext veranschaulicht.The emergence of the digital society has become one of the most pressing research topics in social science. So far political science has been at the margins of the debate being restricted by a rather narrow focus on networked communications. The paper attempts to change this by presenting a more encompassing way to thematize digitalization from within political science. After briefly having criticized the research development in political science the paper reconstructs at length some of the most popular conceptualizations in neighboring disciplines. While we highlight the commonalities and strengths of those approaches in theorizing digitalization, we criticize their rather derivative understanding of democratic practices and the political as such.We go on to propose a modified understanding - labeled the "digital constellation" - that looks at the changing shape of democracy by developing a much more nuanced understanding of the interplay of societies and technology. Finally, the argument is illustrated by a short exemplary analysis of the changes occurring in political representation in the context of digitalization

Brandteknisk riskvärdering, Akademiska Barnsjukhuset I Uppsala

This report is a fire safety evaluation of Uppsala University Children’s hospital which is the largest part of the course Fire safety evaluation VBR054 at Lund University. The report is focused on identifying the current risks. This was accomplished by using various computer programs, experiments and hand calculations. Different measures were developed in order to minimize the risks

Myocardial aging as a T-cell–mediated phenomenon

In recent years, the myocardium has been rediscovered under the lenses of immunology, and lymphocytes have been implicated in the pathogenesis of cardiomyopathies with different etiologies. Aging is an important risk factor for heart diseases, and it also has impact on the immune system. Thus, we sought to determine whether immunological activity would influence myocardial structure and function in elderly mice. Morphological, functional, and molecular analyses revealed that the age-related myocardial impairment occurs in parallel with shifts in the composition of tissue-resident leukocytes and with an accumulation of activated CD4+ Foxp3- (forkhead box P3) IFN-γ+ T cells in the heart-draining lymph nodes. A comprehensive characterization of different aged immune-deficient mouse strains revealed that T cells significantly contribute to age-related myocardial inflammation and functional decline. Upon adoptive cell transfer, the T cells isolated from the mediastinal lymph node (med-LN) of aged animals exhibited increased cardiotropism, compared with cells purified from young donors or from other irrelevant sites. Nevertheless, these cells caused rather mild effects on cardiac functionality, indicating that myocardial aging might stem from a combination of intrinsic and extrinsic (immunological) factors. Taken together, the data herein presented indicate that heart-directed immune responses may spontaneously arise in the elderly, even in the absence of a clear tissue damage or concomitant infection. These observations might shed new light on the emerging role of T cells in myocardial diseases, which primarily affect the elderly population.info:eu-repo/semantics/publishedVersio

Ascites’ neutrophil function is significantly impaired in patients with decompensated cirrhosis but can be restored by autologous plasma incubation

Systemic immune cell dysfunction is a typical feature of liver diseases and increases the risk of bacterial infection, especially spontaneous bacterial peritonitis. We evaluated functional properties of neutrophil granulocytes in blood and ascites of patients both with and without decompensated cirrhosis. We collected blood and ascites samples from 63 patients with cirrhosis and eight without cirrhosis. Phagocytosis activity (PA) and oxidative burst activity (OBA) were evaluated after ex vivo stimulation with E. coli, while fluorescence signals were measured by flow cytometry. Ascites’ neutrophil function tests were repeated after incubation with autologous plasma. Ascites’ neutrophils showed an impaired PA and OBA (median blood PA 98.1% (86.8–99.8) vs. ascites’ PA 50.5% (0.4–97.3), p < 0.0001; median blood OBA 98.7% (27.5–100) vs. ascites’ OBA 27.5% (0.3–96.7), p < 0.0001). Patients with non- cirrhotic ascites showed higher PA but equally suppressed OBA. Ascites’ neutrophil function could be partially restored after incubation with autologous plasma (median increase PA: 22.5% (−49.7 – +93.2), p = 0.002; OBA: 22.8% (−10.4 – +48.8), p = 0.002). Ascites’ neutrophils of patients with cirrhosis are functionally impaired, but could be partially restored after incubation with plasma. Further investigations are needed to identify the factors in ascites that are associated with neutrophils’ function