Population structure of spotted sunfish (Lepomis punctatus) in the Florida Everglades as revealed by DNA microsatellite analysis

Genetic diversity can be used to describe patterns of gene flow within and between local and regional populations. The Florida Everglades experiences seasonal fluctuations in water level that can influence local population extinction and recolonization dynamics. In addition, this expansive wetland has been divided into water management regions by canals and levees. These combined factors can affect genetic diversity and population structure of aquatic organisms in the Everglades. We analyzed allelic variation at six DNA microsatellite loci to examine the population structure of spotted sunfish (Lepomis punctatus) from the Everglades. We tested the hypothesis that recurrent local extinction and recent regional divisions have had an effect on patterns of genetic diversity. No marked differences were observed in comparisons of the heterozygosity values of sites within and among water management units. No evidence of isolation by distance was detected in a gene flow and distance correlation between subpopulations. Confidence intervals for the estimated F-statistic values crossed zero, indicating that there was no significant genetic difference between subpopulations within a region or between regions. Notably, the genetic variation among subpopulations in a water conservation area was greater than variation among regions (Fsp>FPT). These data indicate that the spatial scale of recolonization following local extinction appears to be most important within water management units.

A large-scale dynamic vector and raster data visualization geographic information system based on parallel map tiling

With the exponential increasing demands and uses of GIS data visualization system, such as urban planning, environment and climate change monitoring, weather simulation, hydrographic gauge and so forth, the geospatial vector and raster data visualization research, application and technology has become prevalent. However, we observe that current web GIS techniques are merely suitable for static vector and raster data where no dynamic overlaying layers. While it is desirable to enable visual explorations of large-scale dynamic vector and raster geospatial data in a web environment, improving the performance between backend datasets and the vector and raster applications remains a challenging technical issue. This dissertation is to implement these challenging and unimplemented areas: how to provide a large-scale dynamic vector and raster data visualization service with dynamic overlaying layers accessible from various client devices through a standard web browser, and how to make the large-scale dynamic vector and raster data visualization service as rapid as the static one. To accomplish these, a large-scale dynamic vector and raster data visualization geographic information system based on parallel map tiling and a comprehensive performance improvement solution are proposed, designed and implemented. They include: the quadtree-based indexing and parallel map tiling, the Legend String, the vector data visualization with dynamic layers overlaying, the vector data time series visualization, the algorithm of vector data rendering, the algorithm of raster data re-projection, the algorithm for elimination of superfluous level of detail, the algorithm for vector data gridding and re-grouping and the cluster servers side vector and raster data caching.

Spatiotemporal patterns in community structure of macroinvertebrates inhabiting calcareous periphyton mats

Calcareous floating periphyton mats in the southern Everglades provide habitat for a diverse macroinvertebrate community that has not been well characterized. Our study described this community in an oligotrophic marsh, compared it with the macroinvertebrate community associated with adjacent epiphytic algae attached to macrophytes in the water column, and detected spatial patterns in density and community structure. The floating periphyton mat (floating mat) and epiphytic algae in the water column (submerged epiphyton) were sampled at 4 sites (1 km apart) in northern Shark River Slough, Everglades National Park (ENP), in the early (July) and late (November) wet season. Two perpendicular 90-m transects were established at each site and 100 samples were taken in a nested design. Sites were located in wet-prairie spikerush-dominated sloughs with similar water depths and emergent macrophyte communities. Floating mats were sampled by taking cores (6-cm diameter) that were sorted under magnification to enumerate infauna retained on a 250-μm-mesh sieve and with a maximum dimension >1 mm. Our results showed that floating mats provide habitat for a macroinvertebrate community with higher densities (no. animals/g ash-free dry mass) of Hyalella azteca, Dasyhelea spp., and Cladocera, and lower densities of Chironomidae and Planorbella spp. than communities associated with submerged epiphyton. Densities of the most common taxa increased 3× to 15× from early to late wet season, and community differences between the 2 habitat types became more pronounced. Floating-mat coverage and estimated floating-mat biomass increased 20 to 30% and 30 to 110%, respectively, at most sites in the late wet season. Some intersite variation was observed in individual taxa, but no consistent spatial pattern in any taxon was detected at any scale (from 0.2 m to 3 km). Floating mats and their resident macroinvertebrate communities are important components in the Everglades food web. This community should be included in environmental monitoring programs because degradation and eventual loss of the calcareous periphyton mat is associated with P enrichment in this ecosystem.

Effects of an extreme temperature event on the behavior and age structure of an estuarine top predator, Carcharhinus leucas

The frequency of extreme environmental events is predicted to increase in the future. Understanding the short- and long-term impacts of these extreme events on large-bodied predators will provide insight into the spatial and temporal scales at which acute environmental disturbances in top-down processes may persist within and across ecosystems. Here, we use long-term studies of movements and age structure of an estuarine top predator—juvenile bull sharks Carcharhinus leucas—to identify the effects of an extreme ‘cold snap’ from 2 to 13 January 2010 over short (weeks) to intermediate (months) time scales. Juvenile bull sharks are typically year-round residents of the Shark River Estuary until they reach 3 to 5 yr of age. However, acoustic telemetry revealed that almost all sharks either permanently left the system or died during the cold snap. For 116 d after the cold snap, no sharks were detected in the system with telemetry or captured during longline sampling. Once sharks returned, both the size structure and abundance of the individuals present in the nursery had changed considerably. During 2010, individual longlines were 70% less likely to capture any sharks, and catch rates on successful longlines were 40% lower than during 2006−2009. Also, all sharks caught after the cold snap were young-of-the-year or neonates, suggesting that the majority of sharks in the estuary were new recruits and several cohorts had been largely lost from the nursery. The longer-term impacts of this change in bull shark abundance to the trophic dynamics of the estuary and the importance of episodic disturbances to bull shark population dynamics will require continued monitoring, but are of considerable interest because of the ecological roles of bull sharks within coastal estuaries and oceans.

Enhancement of field emission from multistage structure of carbon nanotube arrays

The field emission measurements for the multistage structured nanotubes (i.e., thin-multiwall and single wall carbon nanotubes grown on multiwall carbon nanotubes) were carried out and a low turn-on field of ~0.45 V/ μm, high emission current of 450 μA at a field of IV/μm and a large field enhancement factor of ~26200 were obtained. The thin multiwall carbon nanotubes (thin-MWNTs) and single wall carbon nanotubes (SWNTs) were grown on the regular arrays of vertically aligned multi wall carbon nanotubes (MWNTs) on porous silicon substrate by Chemical Vapor Deposition (CVD) method. The thin-MWNTs and SWNTs grown on MWNTs in this way have a multistage structure which gives higher enhancement of the electric field and hence the electron field emission.

Labeling large scale social media data using budget-driven One-class SVM classification

The social media classification problems draw more and more attention in the past few years. With the rapid development of Internet and the popularity of computers, there is astronomical amount of information in the social network (social media platforms). The datasets are generally large scale and are often corrupted by noise. The presence of noise in training set has strong impact on the performance of supervised learning (classification) techniques. A budget-driven One-class SVM approach is presented in this thesis that is suitable for large scale social media data classification. Our approach is based on an existing online One-class SVM learning algorithm, referred as STOCS (Self-Tuning One-Class SVM) algorithm. To justify our choice, we first analyze the noise-resilient ability of STOCS using synthetic data. The experiments suggest that STOCS is more robust against label noise than several other existing approaches. Next, to handle big data classification problem for social media data, we introduce several budget driven features, which allow the algorithm to be trained within limited time and under limited memory requirement. Besides, the resulting algorithm can be easily adapted to changes in dynamic data with minimal computational cost. Compared with two state-of-the-art approaches, Lib-Linear and kNN, our approach is shown to be competitive with lower requirements of memory and time.

Parallel and Streaming Truth Discovery in Large-Scale Quantitative Crowdsourcing

ACKNOWLEDGEMENTS This research is based upon work supported in part by the U.S. ARL and U.K. Ministry of Defense under Agreement Number W911NF-06-3-0001, and by the NSF under award CNS-1213140. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views or represent the official policies of the NSF, the U.S. ARL, the U.S. Government, the U.K. Ministry of Defense or the U.K. Government. The U.S. and U.K. Governments are authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation hereon.

Near-bed hydrodynamics and turbulence below a large-scale plunging breaking wave over a mobile barred bed profile

Funded by The research presented in this paper is part of the SINBAD project. Grant Number: STW (12058) and EPSRC (EP/J00507X/1, EP/J005541/1)

Parallel and Streaming Truth Discovery in Large-Scale Quantitative Crowdsourcing

ACKNOWLEDGEMENTS This research is based upon work supported in part by the U.S. ARL and U.K. Ministry of Defense under Agreement Number W911NF-06-3-0001, and by the NSF under award CNS-1213140. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views or represent the official policies of the NSF, the U.S. ARL, the U.S. Government, the U.K. Ministry of Defense or the U.K. Government. The U.S. and U.K. Governments are authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation hereon.

Elucidating the Space-Time Structure of Low Level Warm Season Precipitation Processes in the Southern Appalachian Mountains Using Models and Observations

Light rainfall is the baseline input to the annual water budget in mountainous landscapes through the tropics and at mid-latitudes. In the Southern Appalachians, the contribution from light rainfall ranges from 50-60% during wet years to 80-90% during dry years, with convective activity and tropical cyclone input providing most of the interannual variability. The Southern Appalachians is a region characterized by rich biodiversity that is vulnerable to land use/land cover changes due to its proximity to a rapidly growing population. Persistent near surface moisture and associated microclimates observed in this region has been well documented since the colonization of the area in terms of species health, fire frequency, and overall biodiversity. The overarching objective of this research is to elucidate the microphysics of light rainfall and the dynamics of low level moisture in the inner region of the Southern Appalachians during the warm season, with a focus on orographically mediated processes. The overarching research hypothesis is that physical processes leading to and governing the life cycle of orographic fog, low level clouds, and precipitation, and their interactions, are strongly tied to landform, land cover, and the diurnal cycles of flow patterns, radiative forcing, and surface fluxes at the ridge-valley scale. The following science questions will be addressed specifically: 1) How do orographic clouds and fog affect the hydrometeorological regime from event to annual scale and as a function of terrain characteristics and land cover?; 2) What are the source areas, governing processes, and relevant time-scales of near surface moisture convergence patterns in the region?; and 3) What are the four dimensional microphysical and dynamical characteristics, including variability and controlling factors and processes, of fog and light rainfall? The research was conducted with two major components: 1) ground-based high-quality observations using multi-sensor platforms and 2) interpretive numerical modeling guided by the analysis of the in situ data collection. Findings illuminate a high level of spatial – down to the ridge scale - and temporal – from event to annual scale - heterogeneity in observations, and a significant impact on the hydrological regime as a result of seeder-feeder interactions among fog, low level clouds, and stratiform rainfall that enhance coalescence efficiency and lead to significantly higher rainfall rates at the land surface. Specifically, results show that enhancement of an event up to one order of magnitude in short-term accumulation can occur as a result of concurrent fog presence. Results also show that events are modulated strongly by terrain characteristics including elevation, slope, geometry, and land cover. These factors produce interactions between highly localized flows and gradients of temperature and moisture with larger scale circulations. Resulting observations of DSD and rainfall patterns are stratified by region and altitude and exhibit clear diurnal and seasonal cycles.

Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden

The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were diluted and treated by mild sonication. A 10-ml aliquot of a 1:40 dilution was filtered onto a 0.2-mm-pore-size type GTTP polycarbonate filter (Millipore, Eschborn, Germany). Hybridization and microscopic counting of hybridized and 49,69-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Details of probes and formamide concentrations which were used are listed in futher details.. Means were calculated by using 10 to 20 randomly chosen fields for each filter section, which corresponded to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with probe NON338. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected.

Meiofauna and the structure of the benthic community in the Iberian deep sea basin

1. On the cruises 3 and 15 of R.V. "Meteor" 6 grab samples, and 6 hauls with the 6 m Agassiztrawl were taken and at 2 stations the deep sea camera was lowered. This material gave quantitative results on the meiofauna and minimum counts of the macrofauna. 2. The nematodes constitute nearly 95% of the meiofauna, the copepoda only 2%. With increasing sediment depth the density of animals decrease gradually. In the uppermost centimeter of sediment 42.6% of the meiofauna are found while only 3.7% live in layer 6-7 cm. Meiofauna weight ranges from 0.6-5.7 mg/25 m**2 surface i.e. 0.24-2.8 g/m**2. 3. Mean numbers of individuals and weights show standard errors of 20-30 %. As an approximate average values for further considerations the weight of the meiofauna in the area was taken as 1 g/m**2 4. Quantitative information on the macrofauna is derived from the trawls and the photographs for the actinia Chitonanthus abyssorum only, which is found in the rate of 1 individual/36-72 m**2, but seems to be less abundant generally. 5. Animal density does not decrease steadily from nearshore to offshore biocoenoses, i.e. generally with increasing depth. The decrease is more pronounced for macro- than for meiofauna. For the deep sea the weight proportion of macrofauna : meiofauna is of the order of 1 : 1. 6. With the assumption, that adaptation of metabolism to deep sea conditions is similar in macro- and meiofauna total metabolism of invertebrates is ascribed to meiofauna to more than 80%. 7. The structure of the biocoenosis of the deep sea floor is characterized by the meiofauna living on and in the sediment and by the dominance of sediment feeders in the macrofauna. 8. Considering the large numbets and high partition rates of bacteria a comparative large part of the metabolism in the deep sea sediment must be ascribed to bacteria. This favours the hypothesis, that with increasing depth and decreasing addition of organic material to the sediment, the importance of meiofauna and microorganisms for total metabolism increases. 9. Considering the different modes of food transport to the deep sea environment, i.e. sinking of dead particles, transport by vertical migration of organisms, aggregation of organic particles, adsorption of dissoloved organic substance to inorganic particles, and heterotrophy, the sediment may be assumed to contain more food for invertebrates than the water above the bottom. 10. Suspensions feeders of macrofauna are fixed to hard substrates in the sediment surface. Some of them are shown to bend themselves down to the bottom in underwater photographs. This suggests the idea that some deep sea suspension feeders partly depend on food from the sediment surface, on which they feed directly.

Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis

Background: Esophageal adenocarcinoma (EA) is one of the fastest rising cancers in western countries. Barrett’s Esophagus (BE) is the premalignant precursor of EA. However, only a subset of BE patients develop EA, which complicates the clinical management in the absence of valid predictors. Genetic risk factors for BE and EA are incompletely understood. This study aimed to identify novel genetic risk factors for BE and EA.Methods: Within an international consortium of groups involved in the genetics of BE/EA, we performed the first meta-analysis of all genome-wide association studies (GWAS) available, involving 6,167 BE patients, 4,112 EA patients, and 17,159 representative controls, all of European ancestry, genotyped on Illumina high-density SNP-arrays, collected from four separate studies within North America, Europe, and Australia. Meta-analysis was conducted using the fixed-effects inverse variance-weighting approach. We used the standard genome-wide significant threshold of 5×10-8 for this study. We also conducted an association analysis following reweighting of loci using an approach that investigates annotation enrichment among the genome-wide significant loci. The entire GWAS-data set was also analyzed using bioinformatics approaches including functional annotation databases as well as gene-based and pathway-based methods in order to identify pathophysiologically relevant cellular pathways.Findings: We identified eight new associated risk loci for BE and EA, within or near the CFTR (rs17451754, P=4·8×10-10), MSRA (rs17749155, P=5·2×10-10), BLK (rs10108511, P=2·1×10-9), KHDRBS2 (rs62423175, P=3·0×10-9), TPPP/CEP72 (rs9918259, P=3·2×10-9), TMOD1 (rs7852462, P=1·5×10-8), SATB2 (rs139606545, P=2·0×10-8), and HTR3C/ABCC5 genes (rs9823696, P=1·6×10-8). A further novel risk locus at LPA (rs12207195, posteriori probability=0·925) was identified after re-weighting using significantly enriched annotations. This study thereby doubled the number of known risk loci. The strongest disease pathways identified (P<10-6) belong to muscle cell differentiation and to mesenchyme development/differentiation, which fit with current pathophysiological BE/EA concepts. To our knowledge, this study identified for the first time an EA-specific association (rs9823696, P=1·6×10-8) near HTR3C/ABCC5 which is independent of BE development (P=0·45).Interpretation: The identified disease loci and pathways reveal new insights into the etiology of BE and EA. Furthermore, the EA-specific association at HTR3C/ABCC5 may constitute a novel genetic marker for the prediction of transition from BE to EA. Mutations in CFTR, one of the new risk loci identified in this study, cause cystic fibrosis (CF), the most common recessive disorder in Europeans. Gastroesophageal reflux (GER) belongs to the phenotypic CF-spectrum and represents the main risk factor for BE/EA. Thus, the CFTR locus may trigger a common GER-mediated pathophysiology.

A Scalable General Purpose System for Large-Scale Graph Processing

Graph analytics is an important and computationally demanding class of data analytics. It is essential to balance scalability, ease-of-use and high performance in large scale graph analytics. As such, it is necessary to hide the complexity of parallelism, data distribution and memory locality behind an abstract interface. The aim of this work is to build a scalable graph analytics framework that does not demand significant parallel programming experience based on NUMA-awareness.
The realization of such a system faces two key problems:
(i)~how to develop a scale-free parallel programming framework that scales efficiently across NUMA domains; (ii)~how to efficiently apply graph partitioning in order to create separate and largely independent work items that can be distributed among threads.

Energy efficiency optimization in hardware-constrained large-scale MIMO systems

Large-scale multiple-input multiple-output (MIMO) communication systems can bring substantial improvement in spectral efficiency and/or energy efficiency, due to the excessive degrees-of-freedom and huge array gain. However, large-scale MIMO is expected to deploy lower-cost radio frequency (RF) components, which are particularly prone to hardware impairments. Unfortunately, compensation schemes are not able to remove the impact of hardware impairments completely, such that a certain amount of residual impairments always exists. In this paper, we investigate the impact of residual transmit RF impairments (RTRI) on the spectral and energy efficiency of training-based point-to-point large-scale MIMO systems, and seek to determine the optimal training length and number of antennas which maximize the energy efficiency. We derive deterministic equivalents of the signal-to-noise-and-interference ratio (SINR) with zero-forcing (ZF) receivers, as well as the corresponding spectral and energy efficiency, which are shown to be accurate even for small number of antennas. Through an iterative sequential optimization, we find that the optimal training length of systems with RTRI can be smaller compared to ideal hardware systems in the moderate SNR regime, while larger in the high SNR regime. Moreover, it is observed that RTRI can significantly decrease the optimal number of transmit and receive antennas.