SCALABLE PROCESSING OF MULTIPLE AGGREGATE CONTINUOUS QUERIES

Data Stream Management Systems (DSMSs) were developed to be at the heart of every monitor- ing application. Monitoring applications typically register hundreds of Continuous Queries (CQs) in DSMSs in order to continuously process unbounded data streams to detect events of interest. DSMSs must be designed to efficiently handle unbounded streams with large volumes of data and large numbers of CQs, i.e., exhibit scalability. This need for scalability means that the underlying processing techniques a DSMS adopts should be optimized for high throughput (i.e., tuple output rate). Towards this, two main approaches were proposed in the literature: (1) Multiple Query Opti- mization (MQO) and (2) Scheduling. In this dissertation we focus on optimizing the processing of multiple Aggregate Continuous Queries (ACQs), given their high processing cost and popularity in all monitoring applications. Specifically, in this dissertation, we explore shared processing of ACQs and introduce the con- cept of ’Weaveability’ as an indicator of the potential gains of sharing the processing of ACQs. We develop Weave Share, a multiple ACQs optimizer that considers the different uncorrelated factors of the processing cost, such as the input rate and ACQs’ specifications. In order to fully reap the benefits of the new weave-based optimization techniques, we conceptualize a new underlying ag- gregate operator implementation and realize it in the TriOps framework. TriOps enables adaptive sharing of multiple ACQs that have different window specification, predicates and group-by at- tributes. The properties of the proposed techniques are studied analytically and their performance advantages are experimentally evaluated using simulation and in the context of the AQSIOS DSMS prototype

A River of Voices: Confluences and Cross-Currents in the Discourse of the Colorado River

This dissertation argues that the Colorado River and its watershed face a crisis of representation as privileged nineteenth-century myths portraying the American West as a frontier, garden, and wilderness have limited an understanding of what and whom the river is for. It examines the contribution of tributary voices\u27 or the lesser known perspectives from the region to reveal new lines of thinking about this river and its surroundings as they engage the traditional views of the river shaped by these myths. The voices examined at length in this study include contemporary nature writer Craig Childs, recent female boating narratives by Patricia McCairen, Laurie Buyer, and Louise Teal, and AEURHYC, a Mexican water-users association from the Colorado Delta region. Through an interdisciplinary \u27watershed\u27 approach that draws on ecocritical, bioregional, and rhetorical frameworks, this project considers how these tributary voices appropriate, complicate, and often reject the discourses and genres that have traditionally represented the river and watershed. Negotiating these conventional viewpoints, the tributary voices offer new lines of thinking that reveal the river\u27s importance to a broader range of stakeholders. As impending water shortages threaten the region, this dissertation initiates a much needed conversation about the role literary and rhetorical production has in shaping attitudes and behaviors toward the Colorado and its finite resources.\u2

Novel microRNAs are associated with population divergence in transcriptional response to thermal stress in an intertidal copepod

The role of gene expression in adaptation to differing thermal environments has been assayed extensively. Yet, in most natural systems, analyses of gene expression reveal only one level of the complexity of regulatory machineries. MicroRNAs (miRNAs) are small noncoding RNAs which are key components of many gene regulatory networks, and they play important roles in a variety of cellular pathways by modulating post-transcriptional quantities of mRNA available for protein synthesis. The characterization of miRNA loci and their regulatory dynamics in nonmodel systems are still largely understudied. In this study, we examine the role of miRNAs in response to high thermal stress in the intertidal copepod Tigriopus californicus. Allopatric populations of this species show varying levels of local adaptation with respect to thermal regimes, and previous studies showed divergence in gene expression between populations from very different thermal environments. We examined the transcriptional response to temperature stress in two populations separated by only 8 km by utilizing RNA-seq to quantify both mRNA and miRNA levels. Using the currently available genome sequence, we first describe the repertoire of miRNAs in T. californicus and assess the degree to which transcriptional response to temperature stress is governed by miRNA activity. The two populations showed large differences in the number of genes involved, the magnitude of change in commonly used genes and in the number of miRNAs involved in transcriptional modulation during stress. Our results suggest that an increased level of regulatory network complexity may underlie improved survivorship under thermal stress in one of the populations

Genetic, Morphological and Ecological Relationships Among Populations of the Clam Shrimp, \u3ci\u3eCaenestheriella gynecia\u3c/i\u3e

Little is known about the ecology of the clam shrimp, Caenestheriella gynecia. Caenestheriella gynecia was first discovered in 1939 in a single pool in Oxford, Ohio. Schmidt and Kiviat (2007) reported four new localities of C. gynecia in New York and New Jersey, three within the Hudson Valley of New York and one in northeastern New Jersey. Caenestheriella gynecia may have originated from a very small founder population due possibly to unusual dispersal vectors from its natural range to the west, in Ohio. Egg samples and hatched individuals were obtained from all study sites and specimens were raised in the lab to estimate several growth and survivorship traits. In the field, puddle habitats were observed between the months of May and August where water quality parameters (i.e., dissolved oxygen, temperature, conductivity and pH, and nutrient composition) were recorded. Genetic comparisons across the study sites were made using nuclear DNA sequencing and random amplified polymorphic DNA (RAPD) analysis. The results of this study presented a wide range in the hydro-chemical and physical characteristics of the ephemeral pools in which C. gynecia seem to tolerate. Morphologically, New Jersey and Massachusetts populations possessed meristics counts within the range of those discovered by Mattox in 1950. However, I recommend the placement of the New York population within the Cyzicus genus as their meristic measurements fell outside the range for Caenestheriella. RAPD results revealed the presence of more than one clone in puddles containing C. gynecia although mtDNA sequencing did not reveal any genetic variation within or among populations. The lack of males within C. gynecia\u27s population and low levels of genetic variability support the clonal nature of a strictly parthenogenetic species. These investigations provide a substantial extension of fundamental knowledge of this poorly understood species

On the embryonic and post-embryonic development of Pseudopallene sp. (Arthropoda, Pycnogonida) with special focus on neurogenesis and nervous system differentiation

Diese Arbeit befasst sich mit der Entwicklung der Asselspinne Pseudopallene sp. (Arthropoda, Pycnogonida). Die Morphogenese und Nervensystementwicklung werden mithilfe von Rasterelektronenmikroskopie, Histologie, Immunhistochemie und Genexpressionsstudien untersucht. Während der Proboscisbildung lassen sich keine Anzeichen für ein Labrum erkennen. Aufgrund des Fehlens von Palpen- und Ovigeranlagen und der frühen Entwicklung der Laufbeinsegmente ist kein embryonales Protonymphon-Stadium identifizierbar. Die Evolution verschiedener Larvenformen der Pycnogoniden wird im Hinblick auf phylogenetische Studien diskutiert. Die frühen Prozesse im Neuroektoderm zeigen Ähnlichkeiten zu Eucheliceraten und Myriapoden. Hierzu zählen das Fehlen morphologisch distinkter Zelltypen, die Bildung von Zellinternalisierungszentren, die Immigration vorwiegend post-mitotischer Ganglionzellen mit erhöhter Delta-Genexpression und fast ausschließlich tangentiale Zellteilungen. Anschließend bilden sich pro Neuromer ein Paar Invaginationen, was durch Vergrößerung der apikalen Zellen begleitet wird. Letztere sind aufgrund ihrer hohen Mitoseaktivität, ihres asymmetrischen Teilungsmodus und des anhaltenden Zuwachses der basalen Ganglionzellen als stammzellartige neuronale Vorläuferzellen identifizierbar. Hierauf basierend wird die Validität von stammzellartigen neuronalen Vorläuferzellen als Synapomorphie der Krebse und Insekten diskutiert. Zwei evolutionäre Szenarien zur Arthropoden-Neurogenese werden erörtert. In der post-embryonalen Phase lösen sich die invaginierten Zellregionen vom Ektoderm ab. Sie bilden apikal auf den Ganglien paarige Zellcluster und bleiben mit deren Somacortex über fibrilläre ‚cell streams‘ verbunden. Der weitere Zuwachs an Ganglionzellen und die exklusive Zellproliferation in den cluster-stream-Systemen weisen letztere als post-embryonale neurogenetische Nischen aus. Ähnlichkeiten zu der neurogenetischen Nische im Deutocerebrum der decapoden Krebse werden aufgezeigt.This study addresses aspects of the development of the sea spider Pseudopallene sp. (Arthropoda, Pycnogonida). In order to investigate morphogenesis and nervous system development, a combination of scanning electron microscopy, histology, immunohistochemistry and gene expression studies is used. Embryonic proboscis development shows no signs of a labrum. The lack of palpal and ovigeral limbs and the early anlagen of the walking leg segments lead to the rejection of an embryonized protonymphon stage during Pseudopallene development. The evolution of pycnogonid hatching stages is evaluated in light of recent phylogenetic analyses. Early neurogenesis shares similarities with euchelicerates and myriapods, including the lack of morphologically distinct neuroectodermal cell types, formation of transient cell internalization sites, immigration of mostly post-mitotic ganglion cells with elevated levels of Delta gene expression and predominantly tangentially oriented cell divisions in the neuroectoderm. Subsequently, paired invaginations form in each neuromere, being accompanied by marked enlargement of the apical cells. Due to their high mitotic activity, their asymmetric division mode and a marked cell number increase in the ganglia, the big cells are identified as stem cell-like neuronal precursors. Based on this, the validity of stem cell-like neuronal precursors as synapomorphy of crustaceans and hexapods is discussed. Two scenarios on the evolution of arthropod neurogenesis are presented. During the post-embryonic phase, the invaginating cell regions detach internally and form paired cell clusters at the apical ganglion sides. Each cluster remains connected to the ganglion soma cortex via fibrous cell streams. Increasing ganglion cell numbers and exclusive occurrence of mitoses within the cluster-stream-systems characterize the latter as post-embryonic neurogenic niches. Similarities to the neurogenic niche in the deutocerebrum of decapod crustaceans are discussed

Towards sustainable management of inland waters in Tanzania assessing the ecological integrity of river ecosystems in the upper Pangani river basin (Tanzania)

Dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Science (PhD): Biology) December 2020River ecosystems encompass river channels and its floodplains and form a diverse mosaic of habitats upon which countless species of animals and plants depend for survival. They provide a plethora of services for humans including a source of clean water for domestic and industrial uses, a source of food, a means of waste disposal, transportation, power production, and sites for the pursuit of leisure activities. Yet, they belong to the most threatened ecosystems on earth. Major threats to river ecosystems include habitat degradation, water pollution, flow modification, overexploitation, and invasion by exotic species. This is especially true for (sub) tropical developing countries where intensification of land-use for agriculture and poor disposal of untreated waste have markedly degraded rivers and associated floodplain ecosystems. Nevertheless, a proper understanding of ecosystem functioning and biological diversity is lacking. In this Ph.D., we contribute to bridging this knowledge gap. We investigate different factors that explain biodiversity and ecosystem quality in (afro) tropical river systems and associated temporary pool ecosystems in northeastern-Tanzania by using macroinvertebrates as biological indicators and collecting environmental and biological data at various spatial-temporal scales. Firstly, we assessed how seasonality (i.e., wet and dry seasons) influences macroinvertebrate community structure and water quality conditions (Chapters 1 and 2). An extensive repeated-sampling survey was conducted to measure water quality, macroinvertebrates, and other presumed important environmental variables in the two sub-catchments of the Upper Pangani River Basin (UPRB). We found evidence that water quality conditions and macroinvertebrate assemblages differ between seasons and that these differences are associated with high flow velocity, and runoff carrying sediment and nutrient loads from the catchment area to the river systems during the rainy season. Moreover, our results revealed that chlorophyll-a, oxygen and phosphorous (dry season), nitrogen and turbidity (wet season), and substrate composition and agricultural land-use (both seasons) are important determinants for the variation in macroinvertebrates assemblages between sites. We also attempted to identify indicator taxa linked to specific water quality conditions and found that families Hydropsychidae (Trichoptera), Potamonautidae (Decapoda), Baetidae (Ephemeroptera), and Heptageniidae (Ephemeroptera) showed to be indicator taxa of good water quality conditions, while Hirudinea (Annelida) and Chironomidae (Diptera) appeared to be indicator taxa of poor water quality conditions (Chapter 1). Secondly, we focused on the impact of land-use at different spatial scales on river quality (Chapters 1 and 2). To quantify this we used three different spatial methods of land-use estimation; (i) land-use of the entire watershed area above the monitoring site, (ii) a circular buffer around a monitoring site, and (iii) a circular buffer immediately upstream of a monitoring site, with circular buffers varying from 100m to 2km. The land-use percentage compositions in the dry and wet seasons were quantified using Landsat-8 satellite images with a maximum mapping resolution of 30m. We found that physico-chemical water quality and macroinvertebrate assemblages responded differently to land-uses at different scales in both dry and wet seasons. Nevertheless, the relationships were not always straightforward and clearly scale-dependent, suggesting that the spatial estimate used, and the spatial scale considered can strongly confound the conclusions (Chapter 2). Land-use of the entire watershed area upstream of the monitoring site better explained variation in physico-chemical water quality and macroinvertebrate indices whereas macroinvertebrate abundances showed strong links with more local land-use patterns within 100m and 2km radii. In Chapter 3, we added the main constraint that is not always included in studies of river systems i.e., connectivity and spatial autocorrelation among sites. For this, we use a spatially explicit analysis framework (spatial stream network (SSN) models) to test to what extent dendritic stream network structure affects spatial patterns of benthic macroinvertebrates and water chemistry at the catchment scale. We showed that spatial patterns and spatial autocorrelation exist in stream water chemistry and macroinvertebrate indices at both fine- and broad- spatial scale comprising both flow-connected and flow-unconnected spatial relationships. And that SSN models managed to make good predictions of water chemistry concentrations and macroinvertebrate indices at unsampled sites with estimates of uncertainty. The results highlight the value of SSN models and stress the need to specify spatial dependencies representing the dendritic network structure of river ecosystems. Finally, we assessed to what extent the seasonal connectivity of the river with temporary wetlands in the surrounding landscape is a crucial determinant of aquatic communities and environmental conditions in the floodplain wetlands. This was achieved by comparing environmental conditions and diversity and composition of macroinvertebrate communities from river connected pools with endorheic pools (Chapter 4). Macroinvertebrate communities from the two habitats were clearly differentiated and spatial taxon turnover was the main determinant of variation in community composition among pools. Hydrological connectivity facilitated the migration of fish to the river connected pools which structured the invertebrate community assemblages through selective predation, particularly of large prey such as large branchiopod crustaceans. Based on our dataset we identified indicator taxa for the different habitat types and found no specific fauna unique to river connected pools. Overall, our results suggest monitoring of river systems in wet and dry seasons given the fact that different selective filters limit invertebrate assemblages in both seasons. We recommend the creation of intact riparian buffer zones of at least 60 m from each side of the riverbank to help alleviate some of the observed negative effects of the land-use activities on the river systems. In addition, conservation and management schemes of temporary pools should focus on both river connected and endorheic pools to support high regional diversity. More importantly, SSN models should be used to support river basin management in the region in a rapid and cost-effective way

Aquatic macroinvertebrate biodiversity of lowland rural and urban ponds in Leicestershire

Ponds are common and abundant features in nearly all landscapes typical of European lowland landscapes yet research on freshwater biodiversity has traditionally focussed on larger waterbodies such as lakes and rivers. This has led to an increased need to understand and quantify the biodiversity associated with pond habitats to better inform the active conservation and management of these small waterbodies. This thesis examines the aquatic macroinvertebrate biodiversity (alpha, beta and gamma) and conservation value of 95 ponds in Leicestershire, UK, across a variety of urban and rural landscape types and at a range of spatial scales. In addition, the relative importance of local (physicochemical and biological) and spatial (connectivity) variables in structuring macroinvertebrate communities within ponds is investigated. At a regional scale, the greatest macroinvertebrate biodiversity and conservation value was recorded within meadow ponds compared to urban, agricultural and forest ponds. Spatially, ponds were highly physically and biologically heterogeneous. Temporally (seasonally), invertebrate communities were most dissimilar in meadow and agricultural ponds but assemblages were similar in urban and forest ponds. In urban landscapes, park ponds supported a greater diversity of invertebrates than other urban or garden ponds and typically had a greater conservation value. Garden ponds were the most taxon poor of those investigated. Perennial floodplain meadow ponds supported a greater biodiversity of invertebrates compared to ephemeral meadow ponds although conservation value was similar. Despite regular inundation from the River Soar, ephemeral ponds supported distinct communities compared to perennial meadow ponds. Aquatic macrophytes supported a higher diversity of taxa than other pond mesohabitats across all landscapes studied. Physicochemical factors were identified to be the dominant influence on macroinvertebrate assemblages although, a combination of local and spatial factors best explained the variation in community composition at a regional scale and for meadow ponds. Spatial factors were not identified to significantly influence urban pond communities. This study highlights the ecological importance and conservation value of ponds in rural and anthropogenically disturbed landscapes. Recognition of the significant contribution of ponds to freshwater biodiversity at regional and landscape scales is important for future conservation of pond habitats and will help focus and direct conservation strategies to where they are needed most

THE PROTEOMIC RESPONSE OF THE CARCINUS MAENAS Y-ORGAN OVER THE COURSE OF THE MOLT CYCLE

Molting in arthropods is a complex process governed by regulatory mechanisms that have evolved and adapted over millennia to allow these animals to grow, despite being confined by a hardened exoskeleton. We isolated the molt-regulating Y-organs (YO) from the common shore crab Carcinus maenas at molt stages B, C1-3, C4, and D0 to assess how changes in protein abundances might underline the unique physiology of each of these stages. We found that changes in protein abundance were most notable in the postmolt stages (B and C1-3), where an increase in energy metabolism and the reactive oxygen species stress (ROS) response proteins was observed. An increase in triosephosphate isomerase and transketolase suggest that the postmolt YO is participating in triglycerides storage and is also actively recycling excess ribose sugars manufactured during the YO’s previously activated state. We also propose as mechanism through which ROS-induced release of cyclophilin A may contribute to YO atrophy during postmolt through the remodeling of structural proteins such as collagen. We support the standing observation of YO atrophy during postmolt by drawing attention to hemolymph protein abundances, especially those of cryptocyanin isoforms, which dropped precipitously in intermolt (C4) and remained at low abundances into early premolt (D0). Finally, though our evidence is preliminary, we propose that future investigations into the YO proteome address the significance of the protein glutamate dehydrogenase. Glutamate dehydrogenase, a key enzyme involved in the formation of glutamate, represents a potential nutrient-sensing checkpoint that might be involved in YO activation. Historically, most attention has gone to the acute molt stages, where signaling mechanisms involved in the activation of the YO have been the focus. Here, we present data suggesting that other regulatory mechanism may be governing the atrophy the postmolt YO. A better understanding of crustacean physiology has the potential to benefit ecosystems and economies worldwide

A Quadruple-Based Text Analysis System for History and Philosophy of Science

abstract: Computational tools in the digital humanities often either work on the macro-scale, enabling researchers to analyze huge amounts of data, or on the micro-scale, supporting scholars in the interpretation and analysis of individual documents. The proposed research system that was developed in the context of this dissertation ("Quadriga System") works to bridge these two extremes by offering tools to support close reading and interpretation of texts, while at the same time providing a means for collaboration and data collection that could lead to analyses based on big datasets. In the field of history of science, researchers usually use unstructured data such as texts or images. To computationally analyze such data, it first has to be transformed into a machine-understandable format. The Quadriga System is based on the idea to represent texts as graphs of contextualized triples (or quadruples). Those graphs (or networks) can then be mathematically analyzed and visualized. This dissertation describes two projects that use the Quadriga System for the analysis and exploration of texts and the creation of social networks. Furthermore, a model for digital humanities education is proposed that brings together students from the humanities and computer science in order to develop user-oriented, innovative tools, methods, and infrastructures.Dissertation/ThesisDoctoral Dissertation Biology 201

General embryological information service.

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