Techniques for Lagrangian modelling of dispersion in geophysical flows

Basic concepts and definitions relative to Lagrangian Particle Dispersion Models (LPDMs)for the description of turbulent dispersion are introduced. The study focusses on LPDMs that use as input, for the large scale motion, fields produced by Eulerian models, with the small scale motions described by Lagrangian Stochastic Models (LSMs). The data of two different dynamical model have been used: a Large Eddy Simulation (LES) and a General Circulation Model (GCM). After reviewing the small scale closure adopted by the Eulerian model, the development and implementation of appropriate LSMs is outlined. The basic requirement of every LPDM used in this work is its fullfillment of the Well Mixed Condition (WMC). For the dispersion description in the GCM domain, a stochastic model of Markov order 0, consistent with the eddy-viscosity closure of the dynamical model, is implemented. A LSM of Markov order 1, more suitable for shorter timescales, has been implemented for the description of the unresolved motion of the LES fields. Different assumptions on the small scale correlation time are made. Tests of the LSM on GCM fields suggest that the use of an interpolation algorithm able to maintain an analytical consistency between the diffusion coefficient and its derivative is mandatory if the model has to satisfy the WMC. Also a dynamical time step selection scheme based on the diffusion coefficient shape is introduced, and the criteria for the integration step selection are discussed. Absolute and relative dispersion experiments are made with various unresolved motion settings for the LSM on LES data, and the results are compared with laboratory data. The study shows that the unresolved turbulence parameterization has a negligible influence on the absolute dispersion, while it affects the contribution of the relative dispersion and meandering to absolute dispersion, as well as the Lagrangian correlation.

Estimation of Quasi-Rational DSGE Models

Small-scale dynamic stochastic general equilibrium have been treated as the benchmark of much of the monetary policy literature, given their ability to explain the impact of monetary policy on output, inflation and financial markets. One cause of the empirical failure of New Keynesian models is partially due to the Rational Expectations (RE) paradigm, which entails a tight structure on the dynamics of the system. Under this hypothesis, the agents are assumed to know the data genereting process. In this paper, we propose the econometric analysis of New Keynesian DSGE models under an alternative expectations generating paradigm, which can be regarded as an intermediate position between rational expectations and learning, nameley an adapted version of the "Quasi-Rational" Expectatations (QRE) hypothesis. Given the agents' statistical model, we build a pseudo-structural form from the baseline system of Euler equations, imposing that the length of the reduced form is the same as in the `best' statistical model.

Untersuchung von Mischungs- und Transportprozessen in der oberen Troposphäre - unteren Stratosphäre basierend auf in-situ Spurengasmessungen

Die obere Troposphäre / untere Stratosphäre (UTLS: Upper Troposphere / Lower Stratosphere)ist die Übergangsgregion zwischen den dynamisch, chemisch und mikrophysikalisch sehr verschiedenen untersten Atmosphärenschichten, der Troposphäre und der Stratosphäre. Strahlungsaktive Spurengase, wie zum Beispiel Wasserdampf (H2O), Ozon (O3) oder Kohlenstoffdioxid (CO2), und Wolken in der UTLS beeinflussen das Strahlungsbudget der Atmosphäre und das globale Klima. Mögliche Veränderungen in den Verteilungen und Konzentrationen dieser Spurengase modifizieren den Strahlungsantrieb der Atmosphäre und können zum beobachteten Klimawandel beitragen. Ziel dieser Arbeit ist es, Austausch- und Mischungsprozesse innerhalb der UTLS besser zu verstehen und damit Veränderungen der Spurengaszusammensetzung dieser Region genauer prognostizieren zu können. Grundlage hierfür bilden flugzeuggetragene in-situ Spurengasmessungen in der UTLS, welche während der Flugzeugmesskampagnen TACTS / ESMVal 2012 und AIRTOSS - ICE 2013 durchgeführt wurden. Hierbei wurde bei den Messungen von AIRTOSS - ICE 2013 das im Rahmen dieser Arbeit aufgebaute UMAQS (University of Mainz Airborne QCLbased Spectrometer) - Instrument zur Messung der troposphärischen Spurengase Distickstoffmonoxid (N2O) und Kohlenstoffmonoxid (CO) eingesetzt. Dieses erreicht bei einer zeitlichen Auflösung von 1 s eine Messunsicherheit von 0,39 ppbv und 1,39 ppbv der N2O bzw. CO-Mischungsverhältnisse. Die hohe Zeitauflösung und Messgenauigkeit der N2O- und CO- Daten erlaubt die Untersuchung von kleinskaligen Austauschprozessen zwischen Troposphäre und Stratosphäre im Bereich der Tropopause auf räumlichen Skalen kleiner 200 m. Anhand der N2O-Daten von AIRTOSS - ICE 2013 können in-situ detektierte Zirruspartikel in eisübersättigter Luft oberhalb der N2O-basierten chemischen Tropopause nachgewiesen werden. Mit Hilfe der N2O-CO-Korrelation sowie der Analyse von ECMWF-Modelldaten und der Berechnung von Rückwärtstrajektorien kann deren Existenz auf das irreversible Vermischen von troposphärischen und stratosphärischen Luftmassen zurückgeführt werden. Mit den in-situ Messungen von N2O, CO und CH4 (Methan) von TACTS und ESMVal 2012 werden die großräumigen Spurengasverteilungen bis zu einer potentiellen Temperatur von Theta = 410 K in der extratropischen Stratosphäre untersucht. Hierbei kann eine Verjüngung der Luftmassen in der extratropischen Stratosphäre mit Delta Theta > 30 K (relativ zur dynamischen Tropopause) über den Zeitraum der Messkampagne (28.08.2012 - 27.09.2012) nachgewiesen werden. Die Korrelation von N2O mit O3 zeigt, dass diese Verjüngung aufgrund des verstärkten Eintrages von Luftmassen aus der tropischen unteren Stratosphäre verursacht wird. Diese werden über den flachen Zweig der Brewer-Dobson-Zirkulation auf Zeitskalen von wenigen Wochen in die extratropische Stratosphäre transportiert. Anhandrnder Analyse der CO-O3-Korrelation eines Messfluges vom 30.08.2012 wird das irreversible Einmischen von Luftmassen aus der tropischen Stratosphäre in die Extratropen auf Isentropen mit Theta > 380 K identifiziert. Rückwärtstrajektorien zeigen, dass der Ursprung der eingemischten tropischen Luftmassen im Bereich der sommerlichen Antizyklone des asiatischen Monsuns liegt.

Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Ridurre lo scarto nella pesca con reti da posta: il caso di studio nella AMP delle isole Egadi

Sebbene la selettività nel tramaglio sia assodata, rimangono solitamente catturati dalla rete individui di specie bentoniche che non hanno rilevanza ai fini della commercializzazione ma svolgono ruoli ecologici rilevanti nell'ecosistema marino. Oltre che il danno ecologico, la cattura di invertebrati del benthos costituisce un aggravio di lavoro per i pescatori che impiegano molto tempo per la pulizia delle reti. L'obiettivo generale di questo lavoro è la riduzione della cattura "indesiderata" di invertebrati del benthos, migliorando la selettività ed aumentando ulteriormente la sostenibilità della pesca con il tramaglio. Nello specifico si è voluto sperimentare l'installazione di una "greca" sulla parte terminale del tramaglio. Si tratta di una fascia di rete mono-panno montata alla base dell'attrezzo, prima della lima dei piombi, allo scopo di minimizzare la cattura di specie accessorie e il rischio di danneggiamento degli organismi bentonici. Sono state impiegate 2 imbarcazioni provviste di attrezzo sperimentale in ciascuna delle tre differenti aree di indagine (Favignana, Marettimo, Trapani), per un totale di 48 uscite. Le prove di pesca sono state condotte all’interno dell’Area Marina Protetta Isole Egadi. E’ stato previsto che ogni barca impieghi un attrezzo sperimentale di 1000 metri di lunghezza in cui si alternano 50 metri di tramaglio standard (pannello interno con maglia di 31,25 mm di lato, pannelli esterni con maglia di 180 mm di lato), con pezze delle stesse caratteristiche a cui è stata aggiunta una “greca” di 35 cm di altezza, di maglia di 50 mm di lato. Dal confronto delle catture di specie commerciali e non commerciali ottenute con il tramaglio sperimentale, valutando le differenze di cattura tra le pezze con "greca" e quelle armate in maniera tradizionale, si è osservato che si ha una riduzione degli organismi bentonici nonché delle specie commerciali. L'attrezzo risulta in generale più selettivo nei confronti della rete tradizionale.

Effects of combination therapy with verteporfin photodynamic therapy and ranibizumab in patients with age-related macular degeneration

This open-label, prospective, small-scale study investigated the benefits of same-day verteporfin and intravitreal ranibizumab in patients with predominantly classic, minimally classic or occult subfoveal choroidal neovascularization (CNV) secondary to age-related macular degeneration.

Impact Assessment: Organic Cotton in Jalalabad, Oblast, Kyrgyztan

The aim of the study was to examine the economic performance as well as perceived social and environmental impacts of organic cotton in Southern Kyrgyzstan on the basis of a comparative field study (44 certified organic farmers and 33 conventional farmers) carried out in 2009. It also investigated farmers’ motivation for and assessment of conversion to organic farming. Cotton yields on organic farms were found to be 10% lower whereby input costs per unit were 42% lower, which resulted in organic farmers having a 20% higher revenue from cotton. Due to lower input costs and organic and fair trade price premiums the average gross margin from organic cotton was 27%. In addition to direct economic benefits organic farmers enjoy a number of additional benefits such as easy access to credits on favourable terms, provision with uncontaminated cotton cooking oil and seed cake as animal feed, marketing support as well as extension and training, services provided by the newly established organic service provider. A big majority of organic farmers perceives an improvement of soil qualities, improved health conditions, and positively assesses their previous decision to convert to organic farming. The major disadvantage of organic farming is the high manual labour input required. In the study area, where manual farm work is mainly women’s work and male labour migration widespread, women are most affected by this negative aspect of organic farming. Altogether, the results suggest that despite the inconvenience of higher work load the advantages of organic farming outweigh the disadvantages and that conversion to organic farming can improve the livelihoods of small-scale farmers.

Development of Measurement Methods for Testing of Hydrokinetic Devices to Evaluate the Environmental Effect on Local Substrate

Modifications and upgrades to the hydraulic flume facility in the Environmental Fluid Mechanics and Hydraulics Laboratory (EFM&H) at Bucknell University are described. These changes enable small-scale testing of model marine hydrokinetic(MHK) devices. The design of the experimental platform provides a controlled environment for testing of model MHK devices to determine their effect on localsubstrate. Specifically, the effects being studied are scour and erosion around a cylindrical support structure and deposition of sediment downstream from the device.

Potential and limitations of organic and fair trade cotton for improving livelihoods of smallholders: evidence from Central Asia

Cotton is a leading agricultural non-food commodity associated with soil degradation, water pollution and pesticide poisoning due to high levels of agrochemical inputs. Organic farming is often promoted as a means of addressing the economic, environmental and health risks of conventional cotton production, and it is slowly gaining ground in the global cotton market. Organic and fair trade cotton are widely seen as opportunities for smallholder farmers to improve their livelihoods thanks to higher returns, lower input costs and fewer risks. Despite an increasing number of studies comparing the profitability of organic and non-organic farming systems in developing and industrialized countries, little has been published on organic farming in Central Asia. The aim of this article is to describe the economic performance and perceived social and environmental impacts of organic cotton in southern Kyrgyzstan, drawing on a comparative field study conducted by the author in 2009. In addition to economic and environmental aspects, the study investigated farmers’ motivations toward and assessment of conversion to organic farming. Cotton yields on organic farms were found to be 10% lower, while input costs per unit were 42% lower; as a result, organic farmers’ cotton revenues were 20% higher. Due to lower input costs as well as organic and fair trade price premiums, the average gross margin from organic cotton was 27% higher. In addition to direct economic benefits, organic farmers enjoy other benefits, such as easy access to credit on favorable terms, provision of uncontaminated cottonseed cooking oil and cottonseed cake as animal feed, and marketing support as well as extension and training services provided by newly established organic service providers. The majority of organic farmers perceive improved soil quality, improved health conditions, and positively assess their initial decision to convert to organic farming. The major disadvantage of organic farming is the high manual labor input required. In the study area, where manual farm work is mainly women's work and male labor migration is widespread, women are most affected by this negative aspect of organic farming. Altogether, the results suggest that, despite the inconvenience of a higher workload, the advantages of organic farming outweigh its disadvantages and that conversion to organic farming improves the livelihoods of small-scale farmers.

Simultaneous stable isotope analysis of methane and nitrous oxide on ice core samples

Methane and nitrous oxide are important greenhouse gases which show a strong increase in atmospheric mixing ratios since pre-industrial time as well as large variations during past climate changes. The understanding of their biogeochemical cycles can be improved using stable isotope analysis. However, high-precision isotope measurements on air trapped in ice cores are challenging because of the high susceptibility to contamination and fractionation. Here, we present a dry extraction system for combined CH4 and N2O stable isotope analysis from ice core air, using an ice grating device. The system allows simultaneous analysis of δD(CH4) or δ13C(CH4), together with δ15N(N2O), δ18O(N2O) and δ15N(NO+ fragment) on a single ice core sample, using two isotope mass spectrometry systems. The optimum quantity of ice for analysis is about 600 g with typical "Holocene" mixing ratios for CH4 and N2O. In this case, the reproducibility (1σ ) is 2.1‰ for δD(CH4), 0.18‰ for δ13C(CH4), 0.51‰ for δ15N(N2O), 0.69‰ for δ18O(N2O) and 1.12‰ for δ15N(NO+ fragment). For smaller amounts of ice the standard deviation increases, particularly for N2O isotopologues. For both gases, small-scale intercalibrations using air and/or ice samples have been carried out in collaboration with other institutes that are currently involved in isotope measurements of ice core air. Significant differences are shown between the calibration scales, but those offsets are consistent and can therefore be corrected for.

A Systems-Level Approach to Human Epileptic Seizures

Epileptic seizures are due to the pathological collective activity of large cellular assemblies. A better understanding of this collective activity is integral to the development of novel diagnostic and therapeutic procedures. In contrast to reductionist analyses, which focus solely on small-scale characteristics of ictogenesis, here we follow a systems-level approach, which combines both small-scale and larger-scale analyses. Peri-ictal dynamics of epileptic networks are assessed by studying correlation within and between different spatial scales of intracranial electroencephalographic recordings (iEEG) of a heterogeneous group of patients suffering from pharmaco-resistant epilepsy. Epileptiform activity as recorded by a single iEEG electrode is determined objectively by the signal derivative and then subjected to a multivariate analysis of correlation between all iEEG channels. We find that during seizure, synchrony increases on the smallest and largest spatial scales probed by iEEG. In addition, a dynamic reorganization of spatial correlation is observed on intermediate scales, which persists after seizure termination. It is proposed that this reorganization may indicate a balancing mechanism that decreases high local correlation. Our findings are consistent with the hypothesis that during epileptic seizures hypercorrelated and therefore functionally segregated brain areas are re-integrated into more collective brain dynamics. In addition, except for a special sub-group, a highly significant association is found between the location of ictal iEEG activity and the location of areas of relative decrease of localised EEG correlation. The latter could serve as a clinically important quantitative marker of the seizure onset zone (SOZ).

Computer-assisted liver surgery: clinical applications and technological trends

Oncological liver surgery and interventions aim for removal of tumor tissue while preserving a sufficient amount of functional tissue to ensure organ regeneration. This requires detailed understanding of the patient-specific internal organ anatomy (blood vessel system, bile ducts, tumor location). The introduction of computer support in the surgical process enhances anatomical orientation through patient-specific 3D visualization and enables precise reproduction of planned surgical strategies though stereotactic navigation technology. This article provides clinical background information on indications and techniques for the treatment of liver tumors, reviews the technological contributions addressing the problem of organ motion during navigated surgery on a deforming organ, and finally presents an overview of the clinical experience in computer-assisted liver surgery and interventions. The review concludes that several clinically applicable solutions for computer aided liver surgery are available and small-scale clinical trials have been performed. Further developments will be required more accurate and faster handling of organ deformation and large clinical studies will be required for demonstrating the benefits of computer aided liver surgery.

High Bee and Wasp Diversity in a Heterogeneous Tropical Farming System Compared to Protected Forest

It is a globally important challenge to meet increasing demands for resources and, at the same time, protect biodiversity and ecosystem services. Farming is usually regarded as a major threat to biodiversity due to its expansion into natural areas. We compared biodiversity of bees and wasps between heterogeneous small-scale farming areas and protected forest in northern coastal Belize, Central America. Malaise traps operated for three months during the transition from wet to dry season. Farming areas consisted of a mosaic of mixed crop types, open habitat, secondary forest, and agroforestry. Mean species richness per site (alpha diversity), as well as spatial and temporal community variation (beta diversity) of bees and wasps were equal or higher in farming areas compared to protected forest. The higher species richness and community variation in farmland was due to additional species that did not occur in the forest, whereas most species trapped in forest were also found in farming areas. The overall regional species richness (gamma diversity) increased by 70% with the inclusion of farming areas. Our results suggest that small-scale farming systems adjacent to protected forest may not only conserve, but even favour, biodiversity of some taxonomic groups. We can, however, not exclude possible declines of bee and wasp diversity in more intensified farmland or in landscapes completely covered by heterogeneous farming systems.