Changes in phytoplankton communities and primary production

Lake Victoria is the second largest lake in the world (69000km2) by surface area, but it is the shallowest (69m maximum depth) of the African Great Lakes. It is situated across the equator at an altitude of 1240m and lies in a shallow basin between two uplifted ridges of the eastern and western rift valleys (Beadle 1974). Despite their tropical locations, African lakes exhibit considerable seasonality related to the alteration of warm, wet and cool, dry seasons and the accompanying changes in lucustrine stratification and mixing (Tailing, 1965; 1966; Melack 1979; Hecky& Fee 1981; Hecky& Kling,1981; 1987; Bootsma 1993; Mugidde 1992; 1993). Phytoplankton productivity, biomass and species composition change seasonally in response to variations in light environment and nutrient availability which accompany changes in mixed layer depth and erosion or stabilization of the metalimnion / hypolimnion (Spigel & Coulter 1996; Hecky et al., 1991; Tailing 1987). Over longer, millennial time scales, the phytoplankton communities of the African Great Lakes have responded to variability in the EastAfrican climate (Johnson 1996; Haberyan& Hecky, 1986) which also alters the same ecological factors (Kilham et al., 1986). Recently, over the last few decades, changes in external and or internal factors in Lake Victoria and its basin have had a profound inlluence on the planktic community of this lake (Hecky, 1993; Lipiatou et al., 1996). The lake has experienced 2-10x increases in chlorophyll and 2x increase in primary productivity since Tailing's observations in the early 1960s (Mugidde 1992, 1993). In addition to observed changes in the lake nutrient chemistry (Hecky & Mungoma, 1990; Hecky & Bugenyi 1992; Hecky 1993; Bootsma & Hecky 1993), the deep waters previouslyoxygenated to the sediment surface through most of the year are now regularly anoxic(Hecky et al., 1994).

Technical report on the environmental monitoring of the cage area at the Source of the Nile (SON) Cage Fish Farm for quarter 4: October-December 2015

Source of the Nile (SON) Cage Fish farm is located at Bugungu in Napoleon Gulf, northern Lake Victoria, near the headwaters of the River Nile. NaFIRRI has, through a Public-Private collaborative partnership with SON management, undertaken quarterly monitoring of the cage fish farm since 2011. The objective of the environment monitoring is to track possible environment and biological changes as a result of fish cage operations in the area. The agreed study areas cover selected physical-chemical parameters i.e. water depth, transparency, column temperature, dissolved oxygen, pH and conductivity; nutrient status; and biological parameters i.e. algae, zooplankton, macro-benthos and fish communities. The fourth quarter survey, which is the subject of this report was undertaken during December 2015. Results/observations made are presented in this technical report along with a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and aquatic biota. The present report presents field observations made for the fourth quarter survey undertaken in December 2015 and provides a scientific interpretation and discussion of the results with reference to possible impacts of the cage facilities to the water environment and the different aquatic biota in and around the fish cage site.

Change propagation analysis in complex technical systems

Understanding how and why changes propagate during engineering design is critical because most products and systems emerge from predecessors and not through clean sheet design. This paper applies change propagation analysis methods and extends prior reasoning through examination of a large data set from industry including 41,500 change requests, spanning 8 years during the design of a complex sensor system. Different methods are used to analyze the data and the results are compared to each other and evaluated in the context of previous findings. In particular the networks of connected parent, child and sibling changes are resolved over time and mapped to 46 subsystem areas. A normalized change propagation index (CPI) is then developed, showing the relative strength of each area on the absorber-multiplier spectrum between -1 and +1. Multipliers send out more changes than they receive and are good candidates for more focused change management. Another interesting finding is the quantitative confirmation of the "ripple" change pattern. Unlike the earlier prediction, however, it was found that the peak of cyclical change activity occurred late in the program driven by systems integration and functional testing. Patterns emerged from the data and offer clear implications for technical change management approaches in system design. Copyright © 2007 by ASME.

Changes in the mechanical characteristics of the knee musculature in professional female volleyball players

The technical efficiency in volleyball is closely related to the ability to perform displacements or jump (1). Therefore, it is necessary that precise, individualized, and localized evaluation of the muscles frequently involved in volleyball practice be studied (2,3). The aim of this study was to analyze the neuromuscular changes of the knee musculature in professional volleyball players using Tensiomyography (TMG) and jump tests.

Changes in Web Client Access Patterns: Characteristics and Caching Implications

Understanding the nature of the workloads and system demands created by users of the World Wide Web is crucial to properly designing and provisioning Web services. Previous measurements of Web client workloads have been shown to exhibit a number of characteristic features; however, it is not clear how those features may be changing with time. In this study we compare two measurements of Web client workloads separated in time by three years, both captured from the same computing facility at Boston University. The older dataset, obtained in 1995, is well-known in the research literature and has been the basis for a wide variety of studies. The newer dataset was captured in 1998 and is comparable in size to the older dataset. The new dataset has the drawback that the collection of users measured may no longer be representative of general Web users; however using it has the advantage that many comparisons can be drawn more clearly than would be possible using a new, different source of measurement. Our results fall into two categories. First we compare the statistical and distributional properties of Web requests across the two datasets. This serves to reinforce and deepen our understanding of the characteristic statistical properties of Web client requests. We find that the kinds of distributions that best describe document sizes have not changed between 1995 and 1998, although specific values of the distributional parameters are different. Second, we explore the question of how the observed differences in the properties of Web client requests, particularly the popularity and temporal locality properties, affect the potential for Web file caching in the network. We find that for the computing facility represented by our traces between 1995 and 1998, (1) the benefits of using size-based caching policies have diminished; and (2) the potential for caching requested files in the network has declined.

Changes in the McGurk Effect Across Phonetic Contexts

To investigate the process underlying audiovisual speech perception, the McGurk illusion was examined across a range of phonetic contexts. Two major changes were found. First, the frequency of illusory /g/ fusion percepts increased relative to the frequency of illusory /d/ fusion percepts as vowel context was shifted from /i/ to /a/ to /u/. This trend could not be explained by biases present in perception of the unimodal visual stimuli. However, the change found in the McGurk fusion effect across vowel environments did correspond systematically with changes in second format frequency patterns across contexts. Second, the order of consonants in illusory combination percepts was found to depend on syllable type. This may be due to differences occuring across syllable contexts in the timecourses of inputs from the two modalities as delaying the auditory track of a vowel-consonant stimulus resulted in a change in the order of consonants perceived. Taken together, these results suggest that the speech perception system either fuses audiovisual inputs into a visually compatible percept with a similar second formant pattern to that of the acoustic stimulus or interleaves the information from different modalities, at a phonemic or subphonemic level, based on their relative arrival times.

Bottom-up modelling of energy demand and technical energy savings potential in the Irish residential sector

The International Energy Agency has repeatedly identified increased end-use energy efficiency as the quickest, least costly method of green house gas mitigation, most recently in the 2012 World Energy Outlook, and urges all governing bodies to increase efforts to promote energy efficiency policies and technologies. The residential sector is recognised as a major potential source of cost effective energy efficiency gains. Within the EU this relative importance can be seen from a review of the National Energy Efficiency Action Plans (NEEAP) submitted by member states, which in all cases place a large emphasis on the residential sector. This is particularly true for Ireland whose residential sector has historically had higher energy consumption and CO2 emissions than the EU average and whose first NEEAP targeted 44% of the energy savings to be achieved in 2020 from this sector. This thesis develops a bottom-up engineering archetype modelling approach to analyse the Irish residential sector and to estimate the technical energy savings potential of a number of policy measures. First, a model of space and water heating energy demand for new dwellings is built and used to estimate the technical energy savings potential due to the introduction of the 2008 and 2010 changes to part L of the building regulations governing energy efficiency in new dwellings. Next, the author makes use of a valuable new dataset of Building Energy Rating (BER) survey results to first characterise the highly heterogeneous stock of existing dwellings, and then to estimate the technical energy savings potential of an ambitious national retrofit programme targeting up to 1 million residential dwellings. This thesis also presents work carried out by the author as part of a collaboration to produce a bottom-up, multi-sector LEAP model for Ireland. Overall this work highlights the challenges faced in successfully implementing both sets of policy measures. It points to the wide potential range of final savings possible from particular policy measures and the resulting high degree of uncertainty as to whether particular targets will be met and identifies the key factors on which the success of these policies will depend. It makes recommendations on further modelling work and on the improvements necessary in the data available to researchers and policy makers alike in order to develop increasingly sophisticated residential energy demand models and better inform policy.

Carbon leakage revisited: unilateral climate policy with directed technical change

Using a stylized theoretical model, we argue that current economic analyses of climate policy tend to over-estimate the degree of carbon leakage, as they abstract from the effects of induced technological change. We analyse carbon leakage in a two-country model with directed technical change, where only one of the countries enforces an exogenous cap on emissions. Climate policy induces changes in relative prices, that cause carbon leakage through a terms-of-trade effect. However, these changes in relative prices also affect the incentives to innovate in different sectors. This leads to a counterbalancing induced-technology effect, which always reduces carbon leakage. We therefore conclude that the leakage rates reported in the literature may be too high, as these estimates neglect the effect of price changes on the incentives to innovate.

Development of metabolic labeling strategies to study changes in protein expression

Résumé : Les progrès techniques de la spectrométrie de masse (MS) ont contribué au récent développement de la protéomique. Cette technique peut actuellement détecter, identifier et quantifier des milliers de protéines. Toutefois, elle n'est pas encore assez puissante pour fournir une analyse complète des modifications du protéome corrélées à des phénomènes biologiques. Notre objectif était le développement d'une nouvelle stratégie pour la détection spécifique et la quantification des variations du protéome, basée sur la mesure de la synthèse des protéines plutôt que sur celle de la quantité de protéines totale. Pour cela, nous volions associer le marquage pulsé des protéines par des isotopes stables avec une méthode d'acquisition MS basée sur le balayage des ions précurseurs (precursor ion scan, ou PIS), afin de détecter spécifiquement les protéines ayant intégré les isotopes et d'estimer leur abondance par rapport aux protéines non marquées. Une telle approche peut identifier les protéines avec les plus hauts taux de synthèse dans une période de temps donnée, y compris les protéines dont l'expression augmente spécifiquement suite à un événement précis. Nous avons tout d'abord testé différents acides aminés marqués en combinaison avec des méthodes PIS spécifiques. Ces essais ont permis la détection spécifique des protéines marquées. Cependant, en raison des limitations instrumentales du spectromètre de masse utilisé pour les méthodes PIS, la sensibilité de cette approche s'est révélée être inférieure à une analyse non ciblée réalisée sur un instrument plus récent (Chapitre 2.1). Toutefois, pour l'analyse différentielle de deux milieux de culture conditionnés par des cellules cancéreuses humaines, nous avons utilisé le marquage métabolique pour distinguer les protéines d'origine cellulaire des protéines non marquées du sérum présentes dans les milieux de culture (Chapitre 2.2). Parallèlement, nous avons développé une nouvelle méthode de quantification nommée IBIS, qui utilise des paires d'isotopes stables d'acides aminés capables de produire des ions spécifiques qui peuvent être utilisés pour la quantification relative. La méthode IBIS a été appliquée à l'analyse de deux lignées cellulaires cancéreuses complètement marquées, mais de manière différenciée, par des paires d'acides aminés (Chapitre 2.3). Ensuite, conformément à l'objectif initial de cette thèse, nous avons utilisé une variante pulsée de l'IBIS pour détecter des modifications du protéome dans des cellules HeLa infectée par le virus humain Herpes Simplex-1 (Chapitre 2.4). Ce virus réprime la synthèse des protéines des cellules hôtes afin d'exploiter leur mécanisme de traduction pour la production massive de virions. Comme prévu, de hauts taux de synthèse ont été mesurés pour les protéines virales détectées, attestant de leur haut niveau d'expression. Nous avons de plus identifié un certain nombre de protéines humaines dont le rapport de synthèse et de dégradation (S/D) a été modifié par l'infection virale, ce qui peut donner des indications sur les stratégies utilisées par les virus pour détourner la machinerie cellulaire. En conclusion, nous avons montré dans ce travail que le marquage métabolique peut être employé de façon non conventionnelle pour étudier des dimensions peu explorées en protéomique. Summary : In recent years major technical advancements greatly supported the development of mass spectrometry (MS)-based proteomics. Currently, this technique can efficiently detect, identify and quantify thousands of proteins. However, it is not yet sufficiently powerful to provide a comprehensive analysis of the proteome changes correlated with biological phenomena. The aim of our project was the development of ~a new strategy for the specific detection and quantification of proteomé variations based on measurements of protein synthesis rather than total protein amounts. The rationale for this approach was that changes in protein synthesis more closely reflect dynamic cellular responses than changes in total protein concentrations. Our starting idea was to couple "pulsed" stable-isotope labeling of proteins with a specific MS acquisition method based on precursor ion scan (PIS), to specifically detect proteins that incorporated the label and to simultaneously estimate their abundance, relative to the unlabeled protein isoform. Such approach could highlight proteins with the highest synthesis rate in a given time frame, including proteins specifically up-regulated by a given biological stimulus. As a first step, we tested different isotope-labeled amino acids in combination with dedicated PIS methods and showed that this leads to specific detection of labeled proteins. Sensitivity, however, turned out to be lower than an untargeted analysis run on a more recent instrument, due to MS hardware limitations (Chapter 2.1). We next used metabolic labeling to distinguish the proteins of cellular origin from a high background of unlabeled (serum) proteins, for the differential analysis of two serum-containing culture media conditioned by labeled human cancer cells (Chapter 2.2). As a parallel project we developed a new quantification method (named ISIS), which uses pairs of stable-isotope labeled amino acids able to produce specific reporter ions, which can be used for relative quantification. The ISIS method was applied to the analysis of two fully, yet differentially labeled cancer cell lines, as described in Chapter 2.3. Next, in line with the original purpose of this thesis, we used a "pulsed" variant of ISIS to detect proteome changes in HeLa cells after the infection with human Herpes Simplex Virus-1 (Chapter 2.4). This virus is known to repress the synthesis of host cell proteins to exploit the translation machinery for the massive production of virions. As expected, high synthesis rates were measured for the detected viral proteins, confirming their up-regulation. Moreover, we identified a number of human proteins whose synthesis/degradation ratio (S/D) was affected by the viral infection and which could provide clues on the strategies used by the virus to hijack the cellular machinery. Overall, in this work, we showed that metabolic labeling can be employed in alternative ways to investigate poorly explored dimensions in proteomics.

Directed Technical Change and International Trade

Recent changes in comparative advantage in the largest OECD economies differ significantly from the predictions of Heckscher-Ohlin-Vanek theory. Japan's rising share of OECD machinery exports and the improvement in the comparative advantage of the USA and Germany in heavy industry were accompanied by growing scarcities of the factors used intensively in the favored sector of each country. Here we examine Acemoglu's (1998, 2002) hypothesis that technical change may be directed toward raising the marginal productivity of abundant factors. Testing this hypothesis with 1970-1992 export data from 14 OECD countries, we find evidence that international comparative advantage was reshaped by innovation biased toward the abundant factors in the largest economies.

Technical note: a simple procedure for removing temporal discontinuities in ERA-Interim upper stratospheric temperatures for use in nudged chemistry-climate model simulations

This note describes a simple procedure for removing unphysical temporal discontinuities in ERA-Interim upper stratospheric global mean temperatures in March 1985 and August 1998 that have arisen due to changes in satellite radiance data used in the assimilation. The derived temperature adjustments (offsets) are suitable for use in stratosphere-resolving chemistry-climate models that are nudged (relaxed) to ERA-Interim winds and temperatures. Simulations using a nudged version of the Canadian Middle Atmosphere Model (CMAM) show that the inclusion of the temperature adjustments produces temperature time series that are devoid of the large jumps in 1985 and 1998. Due to its strong temperature dependence, the simulated upper stratospheric ozone is also shown to vary smoothly in time, unlike in a nudged simulation without the adjustments where abrupt changes in ozone occur at the times of the temperature jumps. While the adjustments to the ERA-Interim temperatures remove significant artefacts in the nudged CMAM simulation, spurious transient effects that arise due to water vapour and persist for about 5 yr after the 1979 switch to ERA-Interim data are identified, underlining the need for caution when analysing trends in runs nudged to reanalyses.

Changes on emitter discharge under different water temperature and pressure

The study was conducted at the Research Laboratory of Hydraulic and Irrigation Group in the Rural Engineering Department, Technical University of Madrid (Universidad Politecnica de Madrid), Madrid, Spain. Water temperatures of 20, 30, 40 degrees C and system pressures often encountered in irrigation practices of 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190 and 200 k Pa were applied to determine the effects of different water temperatures and pressures on emitter discharge. Non-pressure compensating in-line emitter which has turbulent flow regime with a long-path (labyrinth), emitter discharge was 4 L h(-1) at system pressure of 100 kPa according to the manufacturer recommended, was used. Emitters were spaced 20 cm along the drip laterals with 16 mm diameter. Discharge equations and coefficients of variation related to temperatures of 20, 30 and 40 degrees C were obtained as q = 0.375H(0.51), q = 0.358H(0.52), q = 0.346H(0.53) and 2.68, 2.09, 3.65, respectively. Discharge of the emitter was affected by different system pressures and increased as potentially (R = 0993-0996). In general. the emitter discharge increased with increasing temperature. However, especially in the common system pressures of 90-120 k Pa, differences of obtained emitter discharges between the different water temperatures were not significant (1%).