Spatial patterns of fish communities along two estuarine gradients in southern Florida

In tropical and subtropical estuaries, gradients of primary productivity and salinity are generally invoked to explain patterns in community structure and standing crops of fishes. We documented spatial and temporal patterns in fish community structure and standing crops along salinity and nutrient gradients in two subtropical drainages of Everglades National Park, USA. The Shark River drains into the Gulf of Mexico and experiences diurnal tides carrying relatively nutrient enriched waters, while Taylor River is more hydrologically isolated by the oligohaline Florida Bay and experiences no discernable lunar tides. We hypothesized that the more nutrient enriched system would support higher standing crops of fishes in its mangrove zone. We collected 50 species of fish from January 2000 to April 2004 at six sampling sites spanning fresh to brackish salinities in both the Shark and Taylor River drainages. Contrary to expectations, we observed lower standing crops and density of fishes in the more nutrient rich tidal mangrove forest of the Shark River than in the less nutrient rich mangrove habitats bordering the Taylor River. Tidal mangrove habitats in the Shark River were dominated by salt-tolerant fish and displayed lower species richness than mangrove communities in the Taylor River, which included more freshwater taxa and yielded relatively higher richness. These differences were maintained even after controlling for salinity at the time of sampling. Small-scale topographic relief differs between these two systems, possibly created by tidal action in the Shark River. We propose that this difference in topography limits movement of fishes from upstream marshes into the fringing mangrove forest in the Shark River system, but not the Taylor River system. Understanding the influence of habitat structure, including connectivity, on aquatic communities is important to anticipate effects of construction and operational alternatives associated with restoration of the Everglades ecosystem.

Does landscape context affect habitat value? The importance of seascape ecology in back-reef systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Mixed spatial and nonspatial problems in location based services

With hundreds of millions of users reporting locations and embracing mobile technologies, Location Based Services (LBSs) are raising new challenges. In this dissertation, we address three emerging problems in location services, where geolocation data plays a central role. First, to handle the unprecedented growth of generated geolocation data, existing location services rely on geospatial database systems. However, their inability to leverage combined geographical and textual information in analytical queries (e.g. spatial similarity joins) remains an open problem. To address this, we introduce SpsJoin, a framework for computing spatial set-similarity joins. SpsJoin handles combined similarity queries that involve textual and spatial constraints simultaneously. LBSs use this system to tackle different types of problems, such as deduplication, geolocation enhancement and record linkage. We define the spatial set-similarity join problem in a general case and propose an algorithm for its efficient computation. Our solution utilizes parallel computing with MapReduce to handle scalability issues in large geospatial databases. Second, applications that use geolocation data are seldom concerned with ensuring the privacy of participating users. To motivate participation and address privacy concerns, we propose iSafe, a privacy preserving algorithm for computing safety snapshots of co-located mobile devices as well as geosocial network users. iSafe combines geolocation data extracted from crime datasets and geosocial networks such as Yelp. In order to enhance iSafe's ability to compute safety recommendations, even when crime information is incomplete or sparse, we need to identify relationships between Yelp venues and crime indices at their locations. To achieve this, we use SpsJoin on two datasets (Yelp venues and geolocated businesses) to find venues that have not been reviewed and to further compute the crime indices of their locations. Our results show a statistically significant dependence between location crime indices and Yelp features. Third, review centered LBSs (e.g., Yelp) are increasingly becoming targets of malicious campaigns that aim to bias the public image of represented businesses. Although Yelp actively attempts to detect and filter fraudulent reviews, our experiments showed that Yelp is still vulnerable. Fraudulent LBS information also impacts the ability of iSafe to provide correct safety values. We take steps toward addressing this problem by proposing SpiDeR, an algorithm that takes advantage of the richness of information available in Yelp to detect abnormal review patterns. We propose a fake venue detection solution that applies SpsJoin on Yelp and U.S. housing datasets. We validate the proposed solutions using ground truth data extracted by our experiments and reviews filtered by Yelp.

Experimental and Analytical Methodologies for Predicting Peak Loads on Building Envelopes and Roofing Systems

The performance of building envelopes and roofing systems significantly depends on accurate knowledge of wind loads and the response of envelope components under realistic wind conditions. Wind tunnel testing is a well-established practice to determine wind loads on structures. For small structures much larger model scales are needed than for large structures, to maintain modeling accuracy and minimize Reynolds number effects. In these circumstances the ability to obtain a large enough turbulence integral scale is usually compromised by the limited dimensions of the wind tunnel meaning that it is not possible to simulate the low frequency end of the turbulence spectrum. Such flows are called flows with Partial Turbulence Simulation. In this dissertation, the test procedure and scaling requirements for tests in partial turbulence simulation are discussed. A theoretical method is proposed for including the effects of low-frequency turbulences in the post-test analysis. In this theory the turbulence spectrum is divided into two distinct statistical processes, one at high frequencies which can be simulated in the wind tunnel, and one at low frequencies which can be treated in a quasi-steady manner. The joint probability of load resulting from the two processes is derived from which full-scale equivalent peak pressure coefficients can be obtained. The efficacy of the method is proved by comparing predicted data derived from tests on large-scale models of the Silsoe Cube and Texas-Tech University buildings in Wall of Wind facility at Florida International University with the available full-scale data. For multi-layer building envelopes such as rain-screen walls, roof pavers, and vented energy efficient walls not only peak wind loads but also their spatial gradients are important. Wind permeable roof claddings like roof pavers are not well dealt with in many existing building codes and standards. Large-scale experiments were carried out to investigate the wind loading on concrete pavers including wind blow-off tests and pressure measurements. Simplified guidelines were developed for design of loose-laid roof pavers against wind uplift. The guidelines are formatted so that use can be made of the existing information in codes and standards such as ASCE 7-10 on pressure coefficients on components and cladding.

Analysis of fractured terrain using remote sensing and geographic information systems : establishing a correlation between fracture network properties and vegetation

This research analyzed the spatial relationship between a mega-scale fracture network and the occurrence of vegetation in an arid region. High-resolution aerial photographs of Arches National Park, Utah were used for digital image processing. Four sets of large-scale joints were digitized from the rectified color photograph in order to characterize the geospatial properties of the fracture network with the aid of a Geographic Information System. An unsupervised landcover classification was carried out to identify the spatial distribution of vegetation on the fractured outcrop. Results of this study confirm that the WNW-ESE alignment of vegetation is dominantly controlled by the spatial distribution of the systematic joint set, which in turn parallels the regional fold axis. This research provides insight into the spatial heterogeneity inherent to fracture networks, as well as the effects of jointing on the distribution of surface vegetation in desert environments.

A method for enhancing digital information displayed to computer users with visual refractive errors via spatial and spectral processing

This research pursued the conceptualization, implementation, and verification of a system that enhances digital information displayed on an LCD panel to users with visual refractive errors. The target user groups for this system are individuals who have moderate to severe visual aberrations for which conventional means of compensation, such as glasses or contact lenses, does not improve their vision. This research is based on a priori knowledge of the user's visual aberration, as measured by a wavefront analyzer. With this information it is possible to generate images that, when displayed to this user, will counteract his/her visual aberration. The method described in this dissertation advances the development of techniques for providing such compensation by integrating spatial information in the image as a means to eliminate some of the shortcomings inherent in using display devices such as monitors or LCD panels. Additionally, physiological considerations are discussed and integrated into the method for providing said compensation. In order to provide a realistic sense of the performance of the methods described, they were tested by mathematical simulation in software, as well as by using a single-lens high resolution CCD camera that models an aberrated eye, and finally with human subjects having various forms of visual aberrations. Experiments were conducted on these systems and the data collected from these experiments was evaluated using statistical analysis. The experimental results revealed that the pre-compensation method resulted in a statistically significant improvement in vision for all of the systems. Although significant, the improvement was not as large as expected for the human subject tests. Further analysis suggest that even under the controlled conditions employed for testing with human subjects, the characterization of the eye may be changing. This would require real-time monitoring of relevant variables (e.g. pupil diameter) and continuous adjustment in the pre-compensation process to yield maximum viewing enhancement.

Coral reef habitat maps derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Coral reef maps at various spatial scales and extents are needed for mapping, monitoring, modelling, and management of these environments. High spatial resolution satellite imagery, pixel <10 m, integrated with field survey data and processed with various mapping approaches, can provide these maps. These approaches have been accurately applied to single reefs (10-100 km**2), covering one high spatial resolution scene from which a single thematic layer (e.g. benthic community) is mapped. This article demonstrates how a hierarchical mapping approach can be applied to coral reefs from individual reef to reef-system scales (10-1000 km**2) using object-based image classification of high spatial resolution images guided by ecological and geomorphological principles. The approach is demonstrated for three individual reefs (10-35 km**2) in Australia, Fiji, and Palau; and for three complex reef systems (300-600 km**2) one in the Solomon Islands and two in Fiji. Archived high spatial resolution images were pre-processed and mosaics were created for the reef systems. Georeferenced benthic photo transect surveys were used to acquire cover information. Field and image data were integrated using an object-based image analysis approach that resulted in a hierarchically structured classification. Objects were assigned class labels based on the dominant benthic cover type, or location-relevant ecological and geomorphological principles, or a combination thereof. This generated a hierarchical sequence of reef maps with an increasing complexity in benthic thematic information that included: 'reef', 'reef type', 'geomorphic zone', and 'benthic community'. The overall accuracy of the 'geomorphic zone' classification for each of the six study sites was 76-82% using 6-10 mapping categories. For 'benthic community' classification, the overall accuracy was 52-75% with individual reefs having 14-17 categories and reef systems 20-30 categories. We show that an object-based classification of high spatial resolution imagery, guided by field data and ecological and geomorphological principles, can produce consistent, accurate benthic maps at four hierarchical spatial scales for coral reefs of various sizes and complexities.

Short-term temporal and spatial variations in physical, optical and biogeochemical parameters in June of 2013 in Alfacs Bay (NW Mediterranean)

With the aim of analyzing the complex physical and biogeochemical interactions at high temporal and spatial resolution in the complex estuarine waters of Alfacs Bay, a beam attenuation-based approach was used as optical proxy of different biogeochemical variables. Thus, the dataset contains the attenuation proxies as well as laboratory results from the analysis of water samples, which were used to validate our approach. In addition, the major physical forcing in the Bay was also measured.

Compilation of 220 sediment core d13C data from the glacial Atlantic Ocean

We compare a compilation of 220 sediment core d13C data from the glacial Atlantic Ocean with three-dimensional ocean circulation simulations including a marine carbon cycle model. The carbon cycle model employs circulation fields which were derived from previous climate simulations. All sediment data have been thoroughly quality controlled, focusing on epibenthic foraminiferal species (such as Cibicidoides wuellerstorfi or Planulina ariminensis) to improve the comparability of model and sediment core carbon isotopes. The model captures the general d13C pattern indicated by present-day water column data and Late Holocene sediment cores but underestimates intermediate and deep water values in the South Atlantic. The best agreement with glacial reconstructions is obtained for a model scenario with an altered freshwater balance in the Southern Ocean that mimics enhanced northward sea ice export and melting away from the zone of sea ice production. This results in a shoaled and weakened North Atlantic Deep Water flow and intensified Antarctic Bottom Water export, hence confirming previous reconstructions from paleoproxy records. Moreover, the modeled abyssal ocean is very cold and very saline, which is in line with other proxy data evidence.

On the eigenvalues of the spatial sign covariance matrix in more than two dimensions

Acknowledgments Alexander Dürre was supported in part by the Collaborative Research Grant 823 of the German Research Foundation. David E. Tyler was supported in part by the National Science Foundation grant DMS-1407751. A visit of Daniel Vogel to David E. Tyler was supported by a travel grant from the Scottish Universities Physics Alliance. The authors are grateful to the editors and referees for their constructive comments.

Scaling multimode fibre IM/DD transmission capacity through spatial-spectral multiplexing

Data centre connections can greatly benefit from parallel transmission channels on one multimode fibre (MMF). Shortwave wavelength division multiplexing (SWDM) achieves parallel transmission through spectral multiplexing. Furthermore, MMFs offer a spatial dimension that should be exploited to increase parallel transmission, albeit in a cost-effective way. In this paper, it is shown that SWDM and spatial multiplexing can be combined in intensity modulation and direct detection MMF transmission systems that use selective offset excitation and mode-selective spatial filtering.

Enterprise management and ERP development:case study of Zoomlion using dynamic enterprise reference grid

The enterprise management approach provides a holistic view of organizations and their related information systems. In order to cope with the globalization, virtualization, and volatile competitive environment, traditional firms are seeking to reconstruct their organizational structures and establish new IS architectures to transform from single autonomous entities into more open enterprises supported by new Enterprise Resource Planning (ERP) systems. This paper reports on ERP engage-abilities within three different enterprise management patterns based on the theoretical foundations of the "Dynamic Enterprise Reference Grid". An exploratory inductive study in Zoomlion using the narrative research approach has been conducted. Also, this research delivers a conceptual framework to demonstrate the adoption of ERP in the three enterprise management structures and points to a new architectural type (ERPIII) for operating in the virtual enterprise paradigm. © 2010 Springer-Verlag.

High spatial and temporal resolution interrogation of fully distributed chirped fiber Bragg grating sensors

A novel interrogation technique for fully distributed linearly chirped fiber Bragg grating (LCFBG) strain sensors with simultaneous high temporal and spatial resolution based on optical time-stretch frequency-domain reflectometry (OTS-FDR) is proposed and experimentally demonstrated. LCFBGs is a promising candidate for fully distributed sensors thanks to its longer grating length and broader reflection bandwidth compared to normal uniform FBGs. In the proposed system, two identical LCFBGs are employed in a Michelson interferometer setup with one grating serving as the reference grating whereas the other serving as the sensing element. Broadband spectral interferogram is formed and the strain information is encoded into the wavelength-dependent free spectral range (FSR). Ultrafast interrogation is achieved based on dispersion-induced time stretch such that the target spectral interferogram is mapped to a temporal interference waveform that can be captured in real-Time using a single-pixel photodector. The distributed strain along the sensing grating can be reconstructed from the instantaneous RF frequency of the captured waveform. High-spatial resolution is also obtained due to high-speed data acquisition. In a proof-of-concept experiment, ultrafast real-Time interrogation of fully-distributed grating sensors with various strain distributions is experimentally demonstrated. An ultrarapid measurement speed of 50 MHz with a high spatial resolution of 31.5 μm over a gauge length of 25 mm and a strain resolution of 9.1 μϵ have been achieved.

Data to Decision in a Dynamic Ocean: Robust Species Distribution Models and Spatial Decision Frameworks

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

Determination of Biomolecular Interdomain Motions using Nuclear Magnetic Resonance

Biological macromolecules can rearrange interdomain orientations when binding to various partners. Interdomain dynamics serve as a molecular mechanism to guide the transitions between orientations. However, our understanding of interdomain dynamics is limited because a useful description of interdomain motions requires an estimate of the probabilities of interdomain conformations, increasing complexity of the problem.

Staphylococcal protein A (SpA) has five tandem protein-binding domains and four interdomain linkers. The domains enable Staphylococcus aureus to evade the host immune system by binding to multiple host proteins including antibodies. Here, I present a study of the interdomain motions of two adjacent domains in SpA. NMR spin relaxation experiments identified a 6-residue flexible interdomain linker and interdomain motions. To quantify the anisotropy of the distribution of interdomain orientations, we measured residual dipolar couplings (RDCs) from the two domains with multiple alignments. The N-terminal domain was directly aligned by a lanthanide ion and not influenced by interdomain motions, so it acted as a reference frame to achieve motional decoupling. We also applied {\it de novo} methods to extract spatial dynamic information from RDCs and represent interdomain motions as a continuous distribution on the 3D rotational space. Significant anisotropy was observed in the distribution, indicating the motion populates some interdomain orientations more than others. Statistical thermodynamic analysis of the observed orientational distribution suggests that it is among the energetically most favorable orientational distributions for binding to antibodies. Thus, the affinity is enhanced by a pre-posed distribution of interdomain orientations while maintaining the flexibility required for function.

The protocol described above can be applied to other biological systems in general. Protein molecule calmodulin and RNA molecule trans-activation response element (TAR) also have intensive interdomain motions with relative small intradomain dynamics. Their interdomain motions were studied using our method based on published RDC data. Our results were consistent with literature results in general. The differences could be due to previous studies' use of physical models, which contain assumptions about potential energy and thus introduced non-experimental information into the interpretations.