United States exploring expedition.

Publisher varies.

CYP2D6: a global analysis of phenotypic and genotypic variation in search of radical cure of Plasmodium vivax malaria

Thesis (Master's)--University of Washington, 2016-06

Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North Africa

The houbara bustard, Chlamydotis undulata, is a declining cryptic desert bird whose range extends from North Africa to Central Asia. Three subspecies are currently recognized by geographical distribution and morphology: C.u.fuertaventurae, C.u.undulata and C.u.macqueenii. We have sequenced 854 bp of mitochondrial control region from 73 birds to describe their population genetic structure with a particular sampling focus on the connectivity between C.u.fuertaventurae and C.u.undulata along the Atlantic seaboard of North Africa. Nucleotide and haplotypic diversity varied among the subspecies being highest in C.u.undulata, lowest in C.u.fuertaventurae and intermediate in C.u.macqueenii. C.u.fuertaventurae and C.u.undulata are paraphyletic and an average nucleotide divergence of 2.08% splits the later from C.u.macqueenii. We estimate that C.u.fuertaventurae and C.u.undulata split from C.u.macqueenii approximately 430 000 years ago. C.u.fuertaventurae and C.u.undulata are weakly differentiated (F-ST = 0.27, N-m = 1.3), indicative of a recent shared history. Archaeological evidence indicates that houbara bustards have been present on the Canary Islands for 130-170 000 years. However, our genetic data point to a more recent separation of C.u.fuertaventurae and C.u.undulata at around 20-25 000 years. Concordant archaeological, climatic opportunities for colonization and genetic data point to a scenario of: (i) initial colonization of the Canary Islands about 130 000 years ago; (ii) a period of secondary contact 19-30 000 years ago homogenizing any pre-existing genetic structure followed by; (iii) a period of relative isolation that persists today.

Predicting population dynamics of weed biological control agents: science or gazing into crystal balls?

Various factors can influence the population dynamics of phytophages post introduction, of which climate is fundamental. Here we present an approach, using a mechanistic modelling package (CLIMEX), that at least enables one to make predictions of likely dynamics based on climate alone. As biological control programs will have minimal funding for basic work (particularly on population dynamics), we show how predictions can be made using a species geographical distribution, relative abundance across its range, seasonal phenology and laboratory rearing data. Many of these data sets are more likely to be available than long-term population data, and some can be incorporated into the exploratory phase of a biocontrol program. Although models are likely to be more robust the more information is available, useful models can be developed using information on species distribution alone. The fitted model estimates a species average response to climate, and can be used to predict likely geographical distribution if introduced, where the agent is likely to be more abundant (i.e. good locations) and more importantly for interpretation of release success, the likely variation in abundance over time due to intra- and inter-year climate variability. The latter will be useful in predicting both the seasonal and long-term impacts of the potential biocontrol agent on the target weed. We believe this tool may not only aid in the agent selection process, but also in the design of release strategies, and for interpretation of post-introduction dynamics and impacts. More importantly we are making testable predictions. If biological control is to become more of a science making and testing such hypothesis will be a key component.

Gram-positive infections in patients with end-stage renal disease

Gram-positive microorganisms, specifically coagulase-negative staphylococci are the most common species recovered from clinical culture specimens of patients with end-stage renal disease. The propensity of coagulase-negative staphylococci (CNS) to cause infection in this patient group has been widely debated. However, it is still unclear how this usually avirulent commensal microorganism produces infection that contributes to high rates of morbidity and mortality in patients with end-stage renal disease. The aim of this thesis was to investigate the rate, geographical distribution, molecular and phenotypic mechanisms of Gram-positive microorganisms associated with infection in renal dialysis patients. In addition, it sought to assess the value of early serological diagnosis of dialysis catheter-associated infection and the effect of antimicrobial treatment regimens on the faecal carriage of enteric microorganisms. In this study, the incidence of haemodialysis catheter-associated infection was established with the Meditrend audit tool. This tool was used to assess the infection outcomes of catheter insertion and management procedures until the catheter was explanted. Introduction of a catheter management protocol decreased the incidence of catheter-related infection. Staphylococcal species recovered from episodes of haemodialysis catheter-associated infection and continuous ambulatory peritoneal dialysis (CAPD)-associated peritonitis were genotyped by determination of macrorestriction profiles with pulsed-field gel electrophoresis. This highlighted horizontal transfer of microorganisms between different patients and the environment. The phenotypic characteristics of these strains were also investigated to determine characteristics that could be used as markers for dialysis catheter-associated infection. The expression of elastase, lipase and esterase by CNS was significantly associated with infection. A rapid enzyme-linked immunosorbent assay incorporating a novel staphylococcal antigen (lipid S) was used to evaluate the early detection of anti-staphylococcal immunoglobulin gamma in patient sera. The comparison of culture positive and culture negative patients demonstrated a steady state of immune activation in both groups. However anti-lipid S serum antibody titres > 1000 were found to be a predictor of infection. The effect on faecal carriage of vancomycin resistant enterococci (VRE) and Clostridium difficile toxins in patients treated with CAPD when empiric cephalosporin therapy was substituted for piperacillin/tazobactam was investigated. The introduction of piperacillin/tazobactam demonstrated a decrease in the faecal carriage of VRE.

Gold mineralisation in the Caledonides of the British Isles with special reference to the Dolgellau Gold-belt, North Wales and the Southern Uplands, Scotland. Available in 2 volumes.

Two aspects of gold mineralisation in the Caledonides of the British Isles have been investigated: gold-telluride mineralisation at Clogau Mine, North Wales; and placer gold mineralisation in the Southern Uplands, Scotland. The primary ore assemblage at Clogau Mine is pyrite, arsenopyrite, cobaltite, pyrrhotine, chalcopyrite, galena, tellurbismuth, tetradymite, altaite, hessite, native gold, wehrlite, hedleyite, native bismuth, bismuthunite and various sulphosalts. The generalised paragenesis is early Fe, Co, Cu, As and S species, and later minerals of Pb, Bi, Ag, Au, Te, Sb. Electron probe micro-analysis (EPMA) of complex telluride-sulphide intergrowths suggests that these intergrowths formed by co-crystallisation/replacement processes and not exsolution. Minor element chemical variation, in the sulphides and tellurides, indicates that antimony and cadmium are preferentially partitioned into telluride minerals. Mineral stability diagrams suggest that during gold deposition log bf aTe2 was between -7.9 and -9.7 and log bf aS2 between -12.4 and -13.8. Co-existing mineral assemblages indicate that the final stages of telluride mineralisation were between c. 250 - 275oC. It is suggested that the high-grade telluride ore shoot was the result of remobilisation of Au, Bi, Ag and Te from low grade mineralisation elsewhere within the vein system, and that gold deposition was brought about by destabilisation of gold chloride complexes by interaction with graphite, sulphides and tellurbismuth. Scanning electron microscopy of planer gold grains from the Southern Uplands, Scotland, indicates that detailed studies on the morphology of placer gold can be used to elucidate the history of gold in the placer environment. In total 18 different morphological characteristics were identified. These were divided on an empirical basis, using the relative degree of mechanical attrition, into proximal and distal characteristics. One morphological characteristic (a porous/spongy surface at high magnification) is considered to be chemical in origin and represent the growth of `new' gold in the placer environment. The geographical distribution of morphological characteristics has been examined and suggests that proximal placer gold is spatially associated with the Loch Doon, Cairsphairn and Fleet granitoids. Quantitative EPMA of the placer gold reveals two compositional populations of placer gold. Examination of the geographical distribution of fineness suggests a loose spatial association between granitoids and low fineness placer gold. Also identified was chemically heterogeneous placer gold. EPMA studies of these heterogeneities allowed estimation of annealing history limits, which suggest that the heterogeneities formed between 150 and 235oC. It is concluded, on the basis of relationships between morphology and composition, that there are two types of placer gold in the Southern Uplands: (i) placer gold which is directly inherited from a hypogene source probably spatially associated with granitoids; and (ii) placer gold that has formed during supergene processes.

The uncertainty of identity toolset:analysing digital traces for user profiling

People manage a spectrum of identities in cyber domains. Profiling individuals and assigning them to distinct groups or classes have potential applications in targeted services, online fraud detection, extensive social sorting, and cyber-security. This paper presents the Uncertainty of Identity Toolset, a framework for the identification and profiling of users from their social media accounts and e-mail addresses. More specifically, in this paper we discuss the design and implementation of two tools of the framework. The Twitter Geographic Profiler tool builds a map of the ethno-cultural communities of a person's friends on Twitter social media service. The E-mail Address Profiler tool identifies the probable identities of individuals from their e-mail addresses and maps their geographical distribution across the UK. To this end, this paper presents a framework for profiling the digital traces of individuals.

Impacts of climate change on Lepidoptera species and communities

In this review, the impacts of climate change on Lepidoptera species and communities are summarized, regarding already registered changes in case of individual species and assemblies, and possible future effects. These include changes in abundance, distribution ranges (altitude above sea level, geographical distribution), phenology (earlier or later flying, number of generations per year). The paper also contains a short description of the observed impacts of single factors and conditions (temperature, atmospheric CO2 concentration, drought, predators and parasitoids, UV-B radiation) affecting the life of moths and butterflies, and recorded monitoring results of changes in the Lepidoptera communities of some observed areas. The review is closed with some theoretical considerations concerning the characteristics of “winner” species and also the features and conditions needed for a successful invasion, conquest of new territories.

Climate change and plankton phenology in freshwater: current trends and future commitments

A solid body of empirical, experimental and theoretical evidence accumulated over recent years indicated that freshwater plankton experienced advance in phenology in response to climate change. Despite rapidly growing evidence for phenological changes, we still lack a comprehensive understanding of how climate change alters plankton phenology in freshwater. To overcome current limitations, we need to shed some light on trends and constraints in current research. The goal of this study is to identify current trends and gaps based on analysis of selected papers, by the help of which we can facilitate further advance in the field. We searched the literature for plankton phenology and confined our search to studies where climate change has been proposed to alter plankton phenology and rates of changes were quantified. We did not restrict our search for empirical ontributions; experimental and theoretical studies were considered as well. In the following we discuss the spatio-temporal setting of selected studies, contributions of different taxonomic groups, emerging methodological constraints, measures of phenological trends; and finally give a list of recommendations on how to improve our understanding in the field. The majority of studies were confined to deep lakes with a skewed geographical distribution toward Central Europe, where scientists have long been engaged in limnology. Despite these findings, recent studies suggest that plankton in running waters may experience change in phenology with similar magnitude. Average rate of advancement in phenology of freshwater plankton exceeded those of the marine plankton and the global average. Increasing study duration was not coupled either with increasing contribution of discontinuous data or with increasing rates of phenological changes. Future studies may benefit from i) delivering longterm data across scientific and political boundaries; ii) extending study sites to broader geographical areas with a more explicit consideration of running waters; iii) applying plankton functional groups; iv) increasing the application of satellite data to quantify phytoplankton bloom phenology; v) extending analyses of time series beyond the spring period; vi) using various metrics to quantify variation in phenology; vii) combining empirical, experimental and theoretical approaches; and last but not least viii) paying more attention to emergence dynamics, nonresponding species and trophic mismatch.

The combined impact of urban heat island, thermal bridge effect of buildings and future climate change on the potential overwintering of Phlebotomus species in a Central European metropolis

Leishmaniasis is one of the most important emerging vector-borne diseases in Western Eurasia. Although winter minimum temperatures limit the present geographical distribution of the vector Phlebotomus species, the heat island effect of the cities and the anthropogenic heat emission together may provide the appropriate environment for the overwintering of sand flies. We studied the climate tempering effect of thermal bridges and the heat island effect in Budapest, Hungary. Thermal imaging was used to measure the heat surplus of heat bridges. The winter heat island effect of the city was evaluated by numerical analysis of the measurements of the Aqua sensor of satellite Terra. We found that the surface temperature of thermal bridges can be at least 3-7 °C higher than the surrounding environment. The heat emission of thermal bridges and the urban heat island effect together can cause at least 10 °C higher minimum ambient temperature in winter nights than the minimum temperature of the peri-urban areas. This milder micro-climate of the built environment can enable the potential overwintering of some important European Phlebotomus species. The anthropogenic heat emission of big cities may explain the observed isolated northward populations of Phlebotomus ariasi in Paris and Phlebotomus neglectus in the agglomeration of Budapest.

A comunidade zooplanctônica como bioindicadora do estado trófico de reservatórios da região semiárida tropical

E utrophication in continental aquatic ecosystems and the following deterioration of water quality are some of the greatest problems to be solved in this century. Due to their own peculiarities reservoirs from semi - arid regions constitute a great challenge to water management because of their greater vulnerability to eutrophication process. I dentification of biolo gical community components that may be used as bioindicators is important to allow an early detection of adverse changes, and also to provide subsidies for management and conservation actions. The aim of the present study is to evaluate the potential of zo oplankton community as bioindicator of the trophic state of two reservoirs belonging to the Piranhas - Açu basin, RN, Brazil: Boqueirão de Parelhas and Passagem das Traíras. Monthly sampling s of both systems were carried out in both systems during the period of January to December. Measurements were performed for temperature, pH, dissolved oxygen and water electrical conductivity besides water samples collection for nutrients, suspended solids, chlorophyll - a and zooplankton analyses. T axonomic composition of zooplankton , density and biomass were analysed. Trophic state index, ABC curves , W statistic and the Calanoida: Cyclopoida ratio were also obtained. The results evidenced that Boqueirão de Parelhas reservoir was a mesotrophic sy stem, and Passagem das Traíras r eservoir was eutrophic. In both reservoirs zooplankton community had low species richness, mostly constituted by tolerant species which have wide geographical distribution, as well the dominance of the rotifers Brachionus havanaensis , B. calyciflo rus and Keratella tropica ; of the calanoid copepods Notodiaptomus cearensis and N. iheringi ; cyclopoid copepod Thermocyclops decipiens, and of the cladocerans Ceriodaphnia cornuta and Diaphanosoma spinulosum . Among the biological indices the ABC curves fo r the zooplankton community indicated a moderate dis turbance in both reservoirs, th e Calanoida: Cyclopoida ration indicated not impacted environments , e xcept during the end of the study to the reservoir Passagem das Traíras . It was concluded that the indices used are good indicators of disturbance and alteration in the community, however they are not good indicators for monitoring the trophic state of the studied reservoirs due to the simultaneous occurrence of other factors selecting species, as the c oncentration of ions and high turbidity, which are part of the reservoir characteristics of semiarid.

Síndrome de Guillain-Barré: epidemiologia, prognóstico e fatores de risco

Introduction. Guillain-Barré syndrome (GBS) is an immune-mediated polyneuropathy and the principal cause of acute neuromuscular paralysis. The most prominent GBS subtypes are: acute inflammatory demyelinating polyneuropathy (AIDP), acute motor axonal neuropathy (AMAN), acute motor-sensory axonal neuropathy (AMSAN) and Fisher syndrome (FS). Differences in geographical distribution of variants have been reported. In Brazil, there are few studies describing the characteristics of GBS, but none on the frequency of GBS variants and their clinical manifestations. Infection-induced aberrant immune response resulting from molecular mimicry and formation of cross-reacting antibodies, contribute to complement activation. Functional biallelic polymorphism in immunoglobulin receptors that influence the affinity of IgG subclasses and the type of immune response have been described, suggesting genetic susceptibility to developing disease. It remains unclear whether individuals carrying different FCGR alleles have differential risk for GBS and⁄or disease severity. The goals of this study were: (1) To characterize GBS and describe the clinical findings in a cohort of patients with GBS from the state of Rio Grande do Norte, Brazil; (2) to determine whether polymorphism in FCGR were associated with development of GBS, and (3) to tease out whether the global gene expression studies could be a tool to identify pathways and transcriptional networks which could be regulated and decrease the time of disease. Methods. Clinical and laboratory data for 149 cases of GBS diagnosed from 1994 to 2013 were analyzed. Genomic DNA and total RNA were extracted from whole blood. Antigangliosides antibodies were determined in the sera. In addition, we also assessed whether FCGR polymorphism are present in GBS (n=141) and blood donors (n=364), and global gene expressions were determined for 12 participants with GBS. Blood samples were collected at the diagnosis and post-recovery. Results. AIDP was the most frequent variant (81.8%) of GBS, followed by AMAN (14.7%) and AMSAN (3.3%). The incidence of GBS was 0.3 ⁄ 100,000 people for the state of Rio Grande do Norte and cases occurred at a younger age. GBS was preceded by infections, with the axonal variant associated with episodes of diarrhea (P = 0.025). Proximal weakness was more frequent in AIDP, and distal weakness predominant in the axonal variant. Compared to 42.4% of cases with AIDP (P<0.0001), 84.6% of cases with the axonal variant had nadir in <10 days. Individuals with the axonal variant took longer to recover deambulation (P<0.0001). The mortality of GBS was 5.3%. A worse outcome was related to an axonal variant (OR17.063; P=0.03) and time required to improve one point in the Hughes functional scale (OR 1.028; P=0.03). The FCGR genotypes and allele frequencies did not differ significantly between the patients with GBS and the controls (FCGR2A p=0.367 and FCGR3A p=0.2430). Global gene expression using RNAseq showed variation in transcript coding for protein isoforms during acute phase of disease. Conclusions. The annual incidence of GBS was 0.3 per 100,00 and there was no seasonal pattern. A predominance of the AIDP variant was seen, and the incidence of the disease decreased with age. The distribution of weakness is a function of the clinical variants, and individuals with the axonal variant had a poorer prognosis. Early diagnosis and variant identification leads to proper intervention decreasing in long-term morbidity. FCGR polymorphisms do not seem to influence susceptibility to GBS in this population. This study found deregulated genes and signs of transcriptional network alterations during the acute and recovery phases in GBS. Identification of pathways altered during disease might be target for immune regulation and with potential to ameliorate symptoms.

(Appendix B) Dinoflagellate cysts in Southeast Pacific Ocean surface sediments

orty-eight surface sediment samples from the southeast (SE) Pacific (25-53°S) are investigated for the determination of the spatial distribution of organic-walled dinoflagellate cysts along the western South American continental margin. Fifty-five different taxa are recorded and reflect oceanic or coastal assemblages. The oceanic assemblages are characterised by low cyst concentrations and the dominance of autotrophs, while the coastal assemblages generally contain a higher number of cysts, which are mainly produced by heterotrophic species. Highest cyst concentrations are observed in the active upwelling system offshore Concepción (35-37°S). Brigantedinium spp., Echinidinium aculeatum, Echinidinium granulatum/delicatum and cysts of Protoperidinium americanum dominate assemblages related to upwelling. Echinidinium aculeatum appears to be the best indicator for the presence of all year round active upwelling cells. Other protoperidinioid cysts may also occur in high relative abundances in coastal regions outside active upwelling systems, if the availability of nutrients, co-responsible for the presence/absence of their main food sources such as diatoms and other protists, is sufficient. The importance of nutrient availability as a determining environmental variable influencing cyst signals on a regional scale (SE Pacific) is demonstrated through statistical analyses of the data. Because of the importance of nutrients, uncertainties about the outcomes of quantitative sea-surface temperature (SST) reconstructions (Modern Analogue Technique) based on dinoflagellate cysts may arise, since no interaction between different hydrographical variables is considered in this approach. The combination of the SE Pacific surface sample dataset with other published cyst data from the Southern Hemisphere resulted in a database which includes 350 samples: the 'SH350 database'. This database is used to test the accuracy of the quantitative reconstructions by calculating and comparing the estimated versus observed values for each site. An attempt to perform quantitative SST reconstructions on the last 25 cal ka of site ODP1233 (41°S; 74°27'W) is made and again stresses the importance of other environmental variables such as nutrient availability in determining the dinoflagellate cyst assemblages.

Ostracode relative abundances and geochemistry in surface sediments from Lake Ohrid

Understanding the ecology of bioindicators such as ostracods is essential in order to reconstruct past environmental and climate change from analysis of fossil assemblages preserved in lake sediment cores. Knowledge of the ecology of ancient Lake Ohrid's ostracod fauna is very limited and open to debate. In advance of the Ohrid ICDP-Drilling project, which has potential to generate high-resolution long-term paleoenvironmental data of global importance in paleoclimate research, we sampled Lake Ohrid and a wide range of habitat types in its surroundings to assess 1) the composition of ostracod assemblages in lakes, springs, streams, and short-lived seasonal water bodies, 2) the geographical distribution of ostracods, and 3) the ecological characteristics of individual ostracod species. In total, 40 species were collected alive, and seven species were preserved as valves and empty carapaces. Of the 40 ostracod species, twelve were endemic to Lake Ohrid. The most common genus in the lake was Candona, represented by 13 living species, followed by Paralimnocythere, represented by five living species. The most frequent species was Cypria obliqua. Species with distinct distributions included Heterocypris incongruens, Candonopsis kingsleii, and Cypria lacustris. The most common species in shallow, flooded areas was H. incongruens, and the most prominent species in ditches was C. kingsleii. C. lacustris was widely distributed in channels, springs, lakes, and rivers. Statistical analyses were performed on a "Lake Ohrid" dataset, comprising the subset of samples from Lake Ohrid alone, and an "entire" dataset comprising all samples collected. The unweighted pair group mean average (UPGMA) clustering was mainly controlled by species-specific depth preferences. Canonical Correspondence Analysis (CCA) with forward selection identified water depth, water temperature, and pH as variables that best explained the ostracod distribution in Lake Ohrid. The lack of significance of conductivity and dissolved oxygen in CCA of Ohrid data highlight the uniformity across the lake of the well-mixed waters. In the entire area, CCA revealed that ostracod distribution was best explained by water depth, salinity, conductivity, pH, and dissolved oxygen. Salinity was probably selected by CCA due to the presence of Eucypris virens and Bradleystrandesia reticulata in short-lived seasonal water bodies. Water depth is an important, although indirect, influence on ostracod species distribution which is probably associated with other factors such as sediment texture and food supply. Some species appeared to be indicators for multiple environmental variables, such as lake level and water temperature.

County Cork: the experience of members of the establishment whose houses were burned in the IRA arson campaign, 1920-23

Between May 1920 and March 1923, there were seventy-three houses belonging to the County Cork establishment burnt down by IRA and anti-treaty forces. More houses were destroyed by this method in Cork than in any other Irish county in the same timeframe. The establishment were targeted by the IRA for their political, military and social persuasions that were essentially in opposition to the nationalist movement. The motivations behind these burnings is examined, the main reasons being reprisals for actions taken by Crown forces, military reasons, loyalty of house owners to the British government and agrarianism. The geographical distribution of these burnings is also provided to reveal how active individual IRA brigades were that operated within the county. Though there were few areas of the county left unaffected by the occurrence of arson attacks, there were higher concentrations of burnings in some areas. The house burnings in County Cork did not conform to the national pattern of house burnings and the reasons for this are explored. This study argues that the presence of Crown forces in Cork and their implementation of an official reprisal policy in January 1921 escalated military conflict, and arson attacks became a key tactic utilised by IRA forces in response to this policy. The aftermath of house burnings for members of the establishment is revealed through the various compensation committees that were formed after both the War of Independence and Civil War. Key sources for this study included personal papers of both the establishment and military figures, IRA witness statements, local and national newspapers, the 1901 and 1911 Irish Censuses, Colonial Office Papers, compensation claims filed with the British government and Irish Free State, and others from archives throughout Ireland and the United Kingdom.