Population structure of chum salmon (Oncorhynchus keta) across the Pacific Rim, determined from microsatellite analysis

The Pacific Rim population structure of chum salmon (Oncorhynchus keta) was examined with a survey of microsatellite variation to describe the distribution of genetic variation and to evaluate whether chum salmon may have originated from two or more glacial refuges following dispersal to newly available habitat after glacial retreat. Variation at 14 microsatellite loci was surveyed for over 53,000 chum salmon sampled from over 380 localities ranging from Korea through Washington State. An index of genetic differentiation, FST, over all populations and loci was 0.033, with individual locus values ranging from 0.009 to 0.104. The most genetically diverse chum salmon were observed from Asia, particularly Japan, whereas chum salmon from the Skeena River and Queen Charlotte Islands in northern British Columbia and those from Washington State displayed the fewest number of alleles compared with chum salmon in other regions. Differentiation in chum salmon allele frequencies among regions and populations within regions was approximately 18 times greater than that of annual variation within populations. A regional structuring of populations was the general pattern observed, with chum salmon spawning in different tributaries within a major river drainage or spawning in smaller rivers in a geographic area generally more similar to each other than to populations in different major river drainages or geographic areas. Population structure of chum salmon on a Pacific Rim basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation, but four possible refuges fit better the observed distribution of genetic variation. The distribution of microsatellite variation of chum salmon on a Pacific Rim basis likely reflects the origins of salmon radiating from refuges after the last glaciation period.

填土边坡水文作用机理与破坏过程研究—以深圳羊宝地填土滑坡为例

A full understanding of failure mechanism, critical hydrological condition, and process of mobilization and deposition of a landslide is essential for optimal design of stabilization measure and forecasting of landslide hazard. This requires a quantitative study of hydrological response of a slope to rainfall through field monitoring, laboratory test and numerical modelling. At 13:40 on September 18, 2002, a fill slope failed following a period of prolonged rain in Shenzhen, resulting in 5 fatalities and 31 injuries. The failed mass with a volume about 2.5×104m3 traveled about 140m on level ground. Field monitoring, laboratory test, theoretical analysis and numerical modelling were carried out to undestand the hydrological response and failure mechanism of this fill slope. This thesis mainly focuses on the following aspects: (1) The hydrological responses and failure processes of slopes under rainfall infiltration were reviewed. Firstly, the factors influencing on the hydrological responses of slopes were analysed. Secondly, the change of stress state of slope soil and modelling methods of slope failure under rainfall infiltration were reviewed. (2) The characteristics of the Yangbaodi landslide and associated rainfall triggering the failure were presented. The failure was characterized by shallow flowslide, due to an increase of ground water table caused by rainfall infiltration. (3) A fully automated instrumentation was carried out to monitor rainfall, and saturated – unsaturated hydrological response of the fill slope, using a raingauge, piezometers, tensiometers and moisture probes. A conceptual hydrogeological model was presented based on field monitoring and borehole data. Analysis of monitoring data showed that the high pore water pressure in fill slope was caused by upward flow of semiconfined groundwater in the moderately decomposed granite. (4) Laboratory and in-situ testing was performed to study the physical and mechanical properties of fills. Isotropically consolidated undrained compression tests and anisotropically consolidated constant shear stress tests were carried out to understand the failure mechanism of the fill slope. It is indicated that loosely compacted soil is of strain-softening behaviour under undrained conditions, accompanied with a rapid increase in excess pore water pressure. In anisotropically consolidated constant shear stress tests, a very small axial strain was required to induce the failure and the excess pore water pressure increased quickly at failure. This indicated that static liquefaction caused by rise in groundwater table due to rainfall infiltration occurred. (5) The hydraulic conductivity of the highly and moderately decomposed granite was estimated using monitering data of pore water pressure. A saturated – unsaturated flow was modeled to study the hydrological response of the fill slope using rainfall records. It was observed that the lagged failure was due to the geological conditions and the discrepancy of hydraulic conductivity of slope soils. The hydraulic conductivity of moderately decomposed granite is relatively higher than the other materials, resulting in a semiconfied groundwater flow in the moderately decomposed granite, and subsequent upward flow into the upper fill layer. When the ground water table in the fill layer was increased to the critical state, the fill slope failed. (6) Numerical exercises were conducted to replay the failure process of the fill slope, based on field monitoring, laboratory and in-situ testing. It was found that the fill slope was mobilized by a rapid transfer of the concentrated shear stress. The movement of failure mass was characterized by viscosity fluid with a gradual increase in velocity. The failure process, including mobilization and subsequent movement and deposition, was studied using numerical methods.

An Historical and Theological Analysis of Campus Crusade for Christ's Evangelistic Practice in Two American University Contexts

This dissertation, an exercise in practical theology, consists of a critical conversation between the evangelistic practice of Campus Crusade for Christ in two American university contexts, Bryan Stone's ecclesiologically grounded theology of evangelism, and William Abraham's eschatologically grounded theology of evangelism. It seeks to provide these evangelizing communities several strategic proposals for a more ecclesiologically and eschatologically grounded practice of evangelism within a university context. The current literature on evangelism is long on evangelistic strategy and activity, but short on theological analysis and reflection. This study focuses on concrete practices, but is grounded in a thick description of two particular contexts (derived from qualitative research methods) and a theological analysis of the ecclesiological and eschatological beliefs embedded within their evangelistic activities. The dissertation provides an historical overview of important figures, ideas, and events that helped mold the practice of evangelism inherited by the two ministries of this study, beginning with the famous Haystack Revival on Williams College in 1806. Both ministries, Campus Crusade for Christ at Bowling Green State University (Ohio) and at Washington State University, inherited an evangelistic practice sorely infected with many of the classic distortions that both Abraham and Stone attempt to correct. Qualitative research methods detail the direction that Campus Crusade for Christ at Bowling Green State University (Ohio) and Washington State University have taken the practice of evangelism they inherited. Applying the analytical categories that emerge from a detailed summary of Stone and Abraham to qualitative data of these two ministries reveals several ways evangelism has morphed in a manner sympathetic to Stone's insistence that the central logic of evangelism is the embodied witness of the church. The results of this analysis reveal the subversive and pervasive influence of modernity on these evangelizing communities—an influence that warrants several corrective strategic proposals including: 1) re-situating evangelism within a reading of the biblical narrative that emphasizes the present, social, public, and realized nature of the gospel of the kingdom of God rather than simply its future, personal, private, and unrealized dimensions; 2) clarifying the nature of the evangelizing communities and their relationship to the church; and 3) emphasizing the virtues that characterize a new evangelistic exemplar who is incarnational, intentional, humble, and courageous.

Hazard and early warning analysis based on domain specific modeling technologies

An aim of proactive risk management strategies is the timely identification of safety related risks. One way to achieve this is by deploying early warning systems. Early warning systems aim to provide useful information on the presence of potential threats to the system, the level of vulnerability of a system, or both of these, in a timely manner. This information can then be used to take proactive safety measures. The United Nation’s has recommended that any early warning system need to have four essential elements, which are the risk knowledge element, a monitoring and warning service, dissemination and communication and a response capability. This research deals with the risk knowledge element of an early warning system. The risk knowledge element of an early warning system contains models of possible accident scenarios. These accident scenarios are created by using hazard analysis techniques, which are categorised as traditional and contemporary. The assumption in traditional hazard analysis techniques is that accidents are occurred due to a sequence of events, whereas, the assumption of contemporary hazard analysis techniques is that safety is an emergent property of complex systems. The problem is that there is no availability of a software editor which can be used by analysts to create models of accident scenarios based on contemporary hazard analysis techniques and generate computer code that represent the models at the same time. This research aims to enhance the process of generating computer code based on graphical models that associate early warning signs and causal factors to a hazard, based on contemporary hazard analyses techniques. For this purpose, the thesis investigates the use of Domain Specific Modeling (DSM) technologies. The contributions of this thesis is the design and development of a set of three graphical Domain Specific Modeling languages (DSML)s, that when combined together, provide all of the necessary constructs that will enable safety experts and practitioners to conduct hazard and early warning analysis based on a contemporary hazard analysis approach. The languages represent those elements and relations necessary to define accident scenarios and their associated early warning signs. The three DSMLs were incorporated in to a prototype software editor that enables safety scientists and practitioners to create and edit hazard and early warning analysis models in a usable manner and as a result to generate executable code automatically. This research proves that the DSM technologies can be used to develop a set of three DSMLs which can allow user to conduct hazard and early warning analysis in more usable manner. Furthermore, the three DSMLs and their dedicated editor, which are presented in this thesis, may provide a significant enhancement to the process of creating the risk knowledge element of computer based early warning systems.

Genetic analysis of the dTDP-rhamnose biosynthesis region of the Escherichia coli VW187 (O7:K1) rfb gene cluster:identification of functional homologs of rfbB and rfbA in the rff cluster and correct location of the rffE gene

The O-repeating unit of the Escherichia coli O7-specific lipopolysaccharide is made of galactose, mannose, rhamnose, 4-acetamido-4,6-dideoxyglucose, and N-acetyglucosamine. We have recently characterized the genes involved in the biosynthesis of the sugar precursor GDP-mannose occurring in the E. coli O7:K1 strain VW187 (C. L. Marolda and M. A. Valvano, J. Bacteriol. 175:148-158, 1993). In the present study, we identified and sequenced the rfbBDAC genes encoding the enzymes for the biosynthesis of another precursor, dTDP-rhamnose. These genes are localized on the upstream end of the rfbEcO7 region, and they are strongly conserved compared with similar genes found in various enteric and nonenteric bacteria. Upstream of rfbB we identified a DNA segment containing the rfb promoter and a highly conserved untranslated leader sequence also present in the promoter regions of other surface polysaccharide gene clusters. Also, we have determined that rfbB and rfbA have homologs, rffG (o355) and rffH (o292), respectively, located on the rff cluster, which is involved in the synthesis of enterobacterial common antigen. We provide biochemical evidence that rffG and rffH encode dTDP-glucose dehydratase and glucose-1-phosphate thymidylyltransferase activities, respectively, and we also show that rffG complemented the rfbB defect in the O7+ cosmid pJHCV32. We also demonstrate that rffG is distinct from rffE and map the rffE gene to the second gene of the rff cluster.

Genetic analysis of the O7-polysaccharide biosynthesis region from the Escherichia coli O7:K1 strain VW187

We recently cloned biosynthesis genes for the O7-lipopolysaccharide (O7-LPS) side chain from the Escherichia coli K-1 strain VW187 (M. A. Valvano, and J. H. Crosa, Infect. Immun. 57:937-943, 1989). To characterize the O7-LPS region, the recombinant cosmids pJHCV31 and pJHCV32 were mutagenized by transposon mutagenesis with Tn3HoHo1, which carries a promoterless lac operon and can therefore generate lacZ transcriptional fusions with target DNA sequences. Cells containing mutated plasmids were examined for their ability to react by coagglutination with O7 antiserum. The LPS pattern profiles of the insertion mutants were also investigated by electrophoresis of cell envelope fractions, followed by silver staining and immunoblotting analysis. These experiments identified three phenotypic classes of mutants and defined a region in the cloned DNA of about 14 kilobase pairs that is essential for O7-LPS expression. Analysis of beta-galactosidase production by cells carrying plasmids with transposon insertions indicated that transcription occurs in only one direction along the O7-LPS region. In vitro transcription-translation experiments revealed that the O7-LPS region encodes at least 16 polypeptides with molecular masses ranging from 20 to 48 kilodaltons. Also, the O7-LPS region in VW187 was mutagenized by homologous recombination with subsets of the cloned O7-LPS genes subcloned into a suicide plasmid vector. O7-LPS-deficient mutants of VW187 were complemented with pJHCV31 and pJHCV32, confirming that these cosmids contain genetic information that is essential for the expression of the O7 polysaccharide.

Landslide susceptibility evaluation and validation at a regional scale

Tese de doutoramento, Geografia (Geografia Física), Universidade de Lisboa, Instituto de Geografia e Ordenamento do Território, 2014

Tsunami Hazard Assessment of the Strait of Juan de Fuca

This study presents and discusses the tsunami hazard posed by an updated CSZ earthquake scenerio to the coastal communities of Port Angeles and Port Townsend, based on the results of a high resolution GeoClaw simulation with 2/3 arc second resolution (about 20.56 meters) surrounding these towns. In addition, we will also present the results of a coarse regional simulation of the Strait of Juan de Fuca. This coarse study encompasses 28 regions that span the Strait’s coast, including the communities of Anacortes, Bellingham, Friday Harbor, and Victoria, BC in addition to extended areas around Port Angeles and Port Townsend. The finest grid for these 28 regions where we collected results had 2 arc sec resolution (around 62 meters). Finally, we will discuss some inherent uncertainties in the specification of the earthquake scenario, the limitations of the GeoClaw model, and the associated uncertainites in the results.

Atividade de morcegos insetívoros (mammalia, chiroptera) no pampa brasileiro: uso de hábitat e sazonalidade

Bats correspond to 20% of the extant mammal species and, with a few exceptions, use echolocation, a spacial orientation system based on emission and analysis of echoes from sound waves, generally ultrasounds. Echolocation was discovered in the 1940 s and since the 1970 s ultrasound detectors have been commercially available, allowing the investigation of several aspects of the natural history and ecology of bats. Passive acoustic monitoring has been frequently used in habitat use studies, predominantly in North America and Europe, by comparing the number of bat passes between different habitat types. This dissertation presents the first evaluation of the spacial and seasonal variation patterns in the activity of insectivorous bats in the Brazilian biome Pampa, in the state of Rio Grande do Sul. Since bat activity can vary according to habitat type, time of year and climatic conditions, the following hypotheses were tested: 1. bat activity varies between different types of habitat; 2. bat activity varies seasonally; 3. bat activity is influenced by temperature, humidity and wind speed. The acoustic samples were taken along fixed transects of 1500 meters, which were monitored monthly from April 2009 to March 2010. Five habitat types were sampled: eucalypts, stream, riparian forest, wetland and grassland. In each sample, the number of bat passes was obtained by using an ultrasound detector Pettersson D230. A total of 1183 bat passes were registered. Greater bat activity levels was observed along large eucalypts (1.93 bat passes/3min) and along a stream (1.61 bat passes/3 min). A riparian forest (0.94 bat passes/3 min) and a wetland area (0.61 bat passes/3 min) exhibited statistically equal levels of activity. Bat passes were fewer in grassland areas (0,16 bat passes/3 min). Bat activity was not correlated with abiotic factors. However, bat activity was significantly low in the colder season, winter, and was similar in autumn, spring and summer. The observed preference for vegetation borders and water courses agrees with reports from other countries and is attributed predominantly to the high prey abundance in these types of environments. Additionally, low activity in the winter is probably a response to the reduced availability of insects, and to lower temperatures. Our results indicate which areas of arboreal vegetation and water courses should be priorities for the conservation of bats and that alterations of these habitat types might negatively influence bat activity in the region

An analysis of the region of the Phocaea dynamical family

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes

mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Ayes). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome. (C) 2012 Elsevier Inc. All rights reserved.

Improved ground motion intensity measures for reliability-based demand analysis of structures

In Performance-Based Earthquake Engineering (PBEE), evaluating the seismic performance (or seismic risk) of a structure at a designed site has gained major attention, especially in the past decade. One of the objectives in PBEE is to quantify the seismic reliability of a structure (due to the future random earthquakes) at a site. For that purpose, Probabilistic Seismic Demand Analysis (PSDA) is utilized as a tool to estimate the Mean Annual Frequency (MAF) of exceeding a specified value of a structural Engineering Demand Parameter (EDP). This dissertation focuses mainly on applying an average of a certain number of spectral acceleration ordinates in a certain interval of periods, Sa,avg (T1,…,Tn), as scalar ground motion Intensity Measure (IM) when assessing the seismic performance of inelastic structures. Since the interval of periods where computing Sa,avg is related to the more or less influence of higher vibration modes on the inelastic response, it is appropriate to speak about improved IMs. The results using these improved IMs are compared with a conventional elastic-based scalar IMs (e.g., pseudo spectral acceleration, Sa ( T(¹)), or peak ground acceleration, PGA) and the advanced inelastic-based scalar IM (i.e., inelastic spectral displacement, Sdi). The advantages of applying improved IMs are: (i ) "computability" of the seismic hazard according to traditional Probabilistic Seismic Hazard Analysis (PSHA), because ground motion prediction models are already available for Sa (Ti), and hence it is possibile to employ existing models to assess hazard in terms of Sa,avg, and (ii ) "efficiency" or smaller variability of structural response, which was minimized to assess the optimal range to compute Sa,avg. More work is needed to assess also "sufficiency" and "scaling robustness" desirable properties, which are disregarded in this dissertation. However, for ordinary records (i.e., with no pulse like effects), using the improved IMs is found to be more accurate than using the elastic- and inelastic-based IMs. For structural demands that are dominated by the first mode of vibration, using Sa,avg can be negligible relative to the conventionally-used Sa (T(¹)) and the advanced Sdi. For structural demands with sign.cant higher-mode contribution, an improved scalar IM that incorporates higher modes needs to be utilized. In order to fully understand the influence of the IM on the seismis risk, a simplified closed-form expression for the probability of exceeding a limit state capacity was chosen as a reliability measure under seismic excitations and implemented for Reinforced Concrete (RC) frame structures. This closed-form expression is partuclarly useful for seismic assessment and design of structures, taking into account the uncertainty in the generic variables, structural "demand" and "capacity" as well as the uncertainty in seismic excitations. The assumed framework employs nonlinear Incremental Dynamic Analysis (IDA) procedures in order to estimate variability in the response of the structure (demand) to seismic excitations, conditioned to IM. The estimation of the seismic risk using the simplified closed-form expression is affected by IM, because the final seismic risk is not constant, but with the same order of magnitude. Possible reasons concern the non-linear model assumed, or the insufficiency of the selected IM. Since it is impossibile to state what is the "real" probability of exceeding a limit state looking the total risk, the only way is represented by the optimization of the desirable properties of an IM.

An evaluation of seismic hazard in La Hispaniola, after the 2010 Haiti earthquake

An evaluation of the seismic hazard in La Hispaniola Island has been carried out, as part of the cooperative project SISMO-HAITI, supported by the Technical University of Madrid (UPM) and developed by several Spanish Universities, the National Observatory of Environment and Vulnerability) ONEV of Haiti, and with contributions from the Puerto Rico Seismic Network (PRSN) and University Seismological Institute of Dominican Republic (ISU). The study was aimed at obtaining results suitable for seismic design purposes. It started with the elaboration of a seismic catalogue for the Hispaniola Island, requiring an exhaustive revision of data reported by more than 20 seismic agencies, apart from these from the PRSN and ISU. The final catalogue contains 96 historical earthquakes and 1690 instrumental events, and it was homogenized to moment magnitude, Mw. Seismotectonic models proposed for the region were revised and a new regional zonation was proposed, taking into account geological andtectonic data, seismicity, focal mechanisms, and GPS observations. In parallel, attenuation models for subduction and crustal zones were revised in previous projects and the most suitable for the Caribbean plate were selected. Then, a seismic hazard analysis was developed in terms of peak ground acceleration, PGA, and spectral accelerations, SA (T), for periods of 0.1, 0.2, 0.5, 1 and 2s, using the Probabilistic Seismic Hazard Assessment (PSHA) methodology. As a result, different hazard maps were obtained for the quoted parameters, together with Uniform Hazard Spectra for Port au Prince and the main cities in the country. Hazard deaggregation was also carried out in these towns, for the target motion given by the PGA and SA (1s) obtained for return periods of 475, 975 and 2475 years. Therefore, the controlling earthquakes for short- and long-period target motions were derived. This study was started a few months after the 2010 earthquake, as a response to an aid request from the Haitian government to the UPM, and the results are available for the definition of the first building code in Haiti.