101 research outputs found
Coastal Erosion at Spratt Bight Beach, San Andrés: A study on its cause and the applicability of the Building with Nature approach
No full textSan Andrés is a Colombian-Caribbean Island located 800 km from the Colombian coast. On its Eastern side there is a barrier reef formation protecting the island from offshore incident waves. Due to the protected environment created by the coral reef, sandy beaches can be formed on the East side of the island. During normal conditions, waves come predominantly form the East (90% of the wave climate), have significant wave height of 2 m and period of 8 s. Besides, San Andrés is situated on the Caribbean hurricane route, which can cause an enormous damage to the island. The storm season at San Andrés is between October and December, which is also when major erosion events take place.The economy of San Andrés is mostly built upon tourism, specially related to its biodiverse ecosystems and Caribbean beaches. The island’s ecological environment is composed by mangroves, seagrasses, and coral reefs, attracting a wide spectrum of fauna and flora to its ecosystems.During the Masterplan for Coastal Erosion (PMEC), San Andrés was pointed out as a location in which coastal erosion is problematic. In a follow-up of this Masterplan, the island was elected to be part of a program in which solutions against coastal erosion would be presented. This research is part of this project, as a parallel trajectory to get a more profound understanding of the system and the possible mitigation measures that could be applied on the island.With increasing urbanization and frequency of extreme weather events, erosion is becoming a problem with which San Andrés and its residents are repeatedly having to deal. Erosion is specially problematic for the Northern part of the island, called Spratt Bight. This region is not only the most densely populated area of the island, but also economically and touristically very important. Its beach presents periodically eroding patterns during storm seasons, when wave action drives the sediment towards the East, decreasing its beach width almost to none. A decreasing beach width has a direct negative impact on tourism, making coastal erosion in Spratt Bight not only a coastal safety problem, but also an economic issue.This study aims to look into the main hydro- and morphological processes driving coastal erosion in Spratt Bight and, using the Building with Nature philosophy, propose a set of solutions to mitigate this problem. To reach this objective data analysis and literature research has been carried out, after which different environmental conditions were modelled using the numerical model Delft3D. During these activities it was found that independently of its direction, waves approaching San Andrés break upon the coral reef and induce a water level set up inside the coral lagoon. The difference in water level in- and outside the lagoon generates a current and sediment transport, which is directed towards the western opening in the coral reef.When the Northern waves approach the island (1.5% of the wave climate), the same water level set-up phenomenon is observed. However, as waves are approaching form the North, they not only break upon the reef, but are also able to enter the sheltered lagoon through the western opening in the coral reef. These waves are able to bend around the reef reaching the shore and the headland on the Northern part of the island, inducing a longshore current and a sediment transport that is southeastward directed. The result is that Northern waves are mostly responsible for a strong westward and erosive sediment transport pattern. These waves are mostly observed between October and March, which coincides with the storm season in San Andrés. Besides, it was found that the Eastern waves are responsible for restoring the (dynamic) equilibrium profile of Spratt Bight Beach. However, this restoring force has a less strong intensity, taking more time to restore the beach than to disrupt its equilibrium.The solutions proposed include seagrass restoration to enhance ecology, restrain sediment transport and attenuate wave heights; the beneficial reuse of dredged material, to nourish Spratt Bight Beach; and finally, the implementation of artificial coral reefs as breakwaters to prevent the newly nourished sediment to be lost from the system. Besides, artificial coral reefs enhance the ecosystem by attracting fauna and flora increasing biodiversity. All proposed solutions have a positive impact on the beaches and therefore on tourism and the economy of the island. This makes them multifunctional solutions, serving the main goal of protecting the beach while at the same time creating benefits for other functions and values in the area. Following in this way the prescriptions of the Building with Nature design approach by van Eekelen and Bouw (2020).Civil Engineerin
Improving pest risk assessment and management through the aid of geospatial information technology standards
No full textDelivery of geospatial information over the Internet for the management of risks from invasive alien species is an increasingly important service. The evolution of information technology standards for geospatial data is a key factor to simplify network publishing and exchange of maps and data. The World Wide Web Consortium (W3C)-geolocation specification is a recent addition that may prove useful for pest risk management. In this article we implement the W3C-geolocation specification and Open Geospatial Consortium (OGC) mapping standards in a Web browser application for smartphones and tablet computers to improve field surveys for alien invasive species. We report our first season field experiences using this tool for online mapping of plant disease outbreaks and host plant occurrence. It is expected that the improved field data collection tools will result in increased data availability and thereby new opportunities for risk assessment, because data-needs and availability are crucial for species distribution modelling and modelbased forecasts of pest establishment potential. Finally, we close with a comment on the future potential of geospatial information standards to enhance the translation from data to decisions regarding pest risks, which should enable earlier detection of emerging risks as well as more robust projections of pest risks in novel areas. The forthcoming standard for processing of geospatial information, the Web Processing Standard (WPS), should open new technological capabilities both for automatic initiation and updating of risk assessment models based on new incoming data, and subsequent early warning
Genealogical typing of Neisseria meningitidis
No full textDespite the increasing popularity of multilocus sequence typing (MLST), the most appropriate method for characterizing bacterial variation and facilitating epidemiological investigations remains a matter of debate. Here, we propose that different typing schemes should be compared on the basis of their power to infer clonal relationships and investigate the utility of sequence data for genealogical reconstruction by exploiting new statistical tools and data from 20 housekeeping loci for 93 isolates of the bacterial pathogen Neisseria meningitidis. Our analysis demonstrated that all but one of the hyperinvasive isolates established by multilocus enzyme electrophoresis and MLST were grouped into one of six genealogical lineages, each of which contained substantial variation. Due to the confounding effect of recombination, evolutionary relationships among these lineages remained unclear, even using 20 loci. Analyses of the seven loci in the standard MLST scheme using the same methods reproduced this classification, but were unable to support finer inferences concerning the relationships between the members within each complex
Lineage specific recombination rates and microevolution in Listeria monocytogenes
No full textBackground: The bacterium Listeria monocytogenes is a saprotroph as well as an opportunistic human foodborne pathogen, which has previously been shown to consist of at least two widespread lineages (termed lineages I and II) and an uncommon lineage (lineage III). While some L. monocytogenes strains show evidence for considerable diversification by homologous recombination, our understanding of the contribution of recombination to L. monocytogenes evolution is still limited. We therefore used
STRUCTURE and ClonalFrame, two programs that model the effect of recombination, to make inferences about the population structure and different aspects of the recombination process in L. monocytogenes. Analyses were performed using sequences for seven loci (including the house-keeping genes gap, prs, purM and ribC, the stress response gene sigB, and the virulence genes actA and inlA) for 195 L. monocytogenes isolates.
Results: Sequence analyses with ClonalFrame and the Sawyer's test showed that recombination is more
prevalent in lineage II than lineage I and is most frequent in two house-keeping genes (ribC and purM) and the two virulence genes (actA and inlA). The relative occurrence of recombination versus point mutation is about six times higher in lineage II than in lineage I, which causes a higher genetic variability in lineage II. Unlike lineage I, lineage II represents a genetically heterogeneous population with a relatively high proportion (30% average) of genetic material imported from external sources. Phylograms, constructed with correcting for recombination, as well as Tajima's D data suggest that both lineages I and II have suffered a population bottleneck.
Conclusion: Our study shows that evolutionary lineages within a single bacterial species can differ
considerably in the relative contributions of recombination to genetic diversification. Accounting for recombination in phylogenetic studies is critical, and new evolutionary models that account for the possibility of changes in the rate of recombination would be required. While previous studies suggested that only L. monocytogenes lineage I has experienced a recent bottleneck, our analyses clearly show that lineage II experienced a bottleneck at about the same time, which was subsequently obscured by abundant
homologous recombination after the lineage II bottleneck. While lineage I and lineage II should be considered separate species from an evolutionary viewpoint, maintaining single species name may be warranted since both lineages cause the same type of human disease
Electron loss and excitation in atom-atom collisions
No full textIn this thesis we consider processes involving collisions of atomic Hydrogen, or a positive ion, with noble gas targets in which the projectile is excited to a discrete state or ionized. Theoretical methods based upon the first Born approximation, the impulse approximation and the pseudostate close-coupling approximation have been used. For sound theoretical reasons it is useful to distinguish between collisions in which the target remains in its ground state, (singly inelastic collisions), from those in which it is excited or ionized (doubly inelastic collisions). Particular attention has been paid to the problem of summing over all final states of the target. One form of the impulse approximation that is used in this thesis requires a knowledge of differential elastic electron-target scattering. To provide this information for noble gas targets a data base of 'best estimates' has been constructed from results published in literature. Also a computer program to calculate elastic electron-noble gas scattering in the static-exchange approximation has been devised. The theoretical basis for this program, which uses the R-matrix method, has been discussed in detail. Applications have been made to the phenomenom of electron loss to the continuum, the theoretical predictions being compared with experimental data for collisions of atomic Hydrogen and positive ions of Carbon, Oxygen and Silicon with gaseous targets of Helium and Argon. Direct excitation of H(1s) to the n = 2 and n = 3 levels in collisions with Helium, Neon, Argon, Krypton and Xenon targets has also been extensively studied. (author)Available from British Library Document Supply Centre-DSC:DXN026954 / BLDSC - British Library Document Supply CentreSIGLEGBUnited Kingdo
Deep sequencing of the Trypanosoma cruzi GP63 surface proteases reveals diversity and diversifying selection among chronic and congenital Chagas disease patients.
No full textBACKGROUND: Chagas disease results from infection with the diploid protozoan parasite Trypanosoma cruzi. T. cruzi is highly genetically diverse, and multiclonal infections in individual hosts are common, but little studied. In this study, we explore T. cruzi infection multiclonality in the context of age, sex and clinical profile among a cohort of chronic patients, as well as paired congenital cases from Cochabamba, Bolivia and Goias, Brazil using amplicon deep sequencing technology. METHODOLOGY/ PRINCIPAL FINDINGS: A 450bp fragment of the trypomastigote TcGP63I surface protease gene was amplified and sequenced across 70 chronic and 22 congenital cases on the Illumina MiSeq platform. In addition, a second, mitochondrial target--ND5--was sequenced across the same cohort of cases. Several million reads were generated, and sequencing read depths were normalized within patient cohorts (Goias chronic, n = 43, Goias congenital n = 2, Bolivia chronic, n = 27; Bolivia congenital, n = 20), Among chronic cases, analyses of variance indicated no clear correlation between intra-host sequence diversity and age, sex or symptoms, while principal coordinate analyses showed no clustering by symptoms between patients. Between congenital pairs, we found evidence for the transmission of multiple sequence types from mother to infant, as well as widespread instances of novel genotypes in infants. Finally, non-synonymous to synonymous (dn:ds) nucleotide substitution ratios among sequences of TcGP63Ia and TcGP63Ib subfamilies within each cohort provided powerful evidence of strong diversifying selection at this locus. CONCLUSIONS/SIGNIFICANCE: Our results shed light on the diversity of parasite DTUs within each patient, as well as the extent to which parasite strains pass between mother and foetus in congenital cases. Although we were unable to find any evidence that parasite diversity accumulates with age in our study cohorts, putative diversifying selection within members of the TcGP63I gene family suggests a link between genetic diversity within this gene family and survival in the mammalian host
Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents
No full textINTRODUCTION: Coronaviruses encode a helicase that is essential for viral replication and represents an excellent antiviral target. However, only a few coronavirus helicase inhibitors have been patented. These patents include drug-like compound SSYA10-001, aryl diketo acids (ADK), and dihydroxychromones. Additionally, adamantane-derived bananins, natural flavonoids, one acrylamide derivative [(E)-3-(furan-2-yl)-N-(4-sulfamoylphenyl)acrylamide], a purine derivative (7-ethyl-8-mercapto-3-methyl-3,7-dihydro-1 H-purine-2,6-dione), and a few bismuth complexes. The IC50 of patented inhibitors ranges between 0.82 μM and 8.95 μM, depending upon the assays used. Considering the urgency of clinical interventions against Coronavirus Disease-19 (COVID-19), it is important to consider developing antiviral portfolios consisting of small molecules.AREAS COVERED: This review examines coronavirus helicases as antiviral targets, and the potential of previously patented and experimental compounds to inhibit the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) helicase.
EXPERT OPINION: Small molecule coronavirus helicase inhibitors represent attractive pharmacological modalities for the treatment of coronaviruses such as SARS-CoV and SARS-CoV-2. Rightfully so, the current emphasis is focused upon the development of vaccines. However, vaccines may not work for everyone and broad-based adoption of vaccinations is an increasingly challenging societal endeavor. Therefore, it is important to develop additional pharmacological antivirals against the highly conserved coronavirus helicases to broadly protect against this and subsequent coronavirus epidemics
L2 creative writers : identities and writing processes
No full textL2 creative writing research is a relatively unchartered area. Pedagogical
discussions on L2 creative writing activities often focus on manifestations of L2
learners' language learning, writing improvement, or expressions of emotion. There
is a lack of research investigating the underlying identities of L2 creative writers as
social agents. The present research targets the L2 creative writers who are interested
and experienced in certain forms of creative writing. It investigates if and how L2
creative writers' emergent identities enacted in their online cognitive writing
activities under particular tasks are mediated by the writers' 'autobiographical
identities' (Clark and Ivanič, 1997) rooted in their life histories.
Fifteen L2 creative writers from diverse sociocultural and academic backgrounds
participated in the research. Firstly, the participants' 'autobiographical identities'
were explored through eliciting their retrospective life-history accounts in in-depth
interviews. Secondly, the research implemented two think-aloud story-writing
sessions (Autobiographical writing & Prompted story-continuation writing) to
capture the writers' emergent identities instantiated in their cognitive writing
processes. Subsequently, the interconnectedness between these two types of
identities was sought.
Two parallel data analyses were conducted: 1) quantitative data coding targeting
all fifteen L2 creative writers and 2) qualitative discussions concentrating on five
selected focal participants. These two levels of analyses together show that the
participants' cognitive writing processes as evinced through their engagement in
these creative writing activities (i.e. their task-situated emergent identities) are
mediated by the writers’ previous participation in multiple discourses and social
worlds up to the moment of writing (i.e. their autobiographical identities formed
throughout their life histories).
The findings suggest certain directions for theory development in L2 creative
writing research as well as in L2 writer identity research. Regarding L2 creative
writing research, L2 teachers' practice could be enhanced by a deeper understanding
of how creative writing is employed by L2 individuals not only for language or
literacy acquisition purposes, but also as a self-empowering tool to achieve particular
social positioning. Secondly, regarding L2 writer identity research, more research
needs to be done regarding this micro and dynamic view of writer identity which
resides in the movements of the writers' emerging thoughts situated in an immediate
creative writing context and mediated by the writers' previous sociocultural
experiences
Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
No full textChlamydia trachomatis is responsible for both trachoma and sexually transmitted infections, causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed phylogeny based on whole-genome sequencing of representative strains of C. trachomatis from both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis shows that predicting phylogenetic structure using ompA, which is traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks any true relationships present. We show that in many instances, ompA is a chimera that can be exchanged in part or as a whole both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, which is another key diagnostic target. We used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b
Crystal structure and investigation of Bi2TeO6·nH2O (0 ≤ n ≤ 2/3): natural and synthetic montanite
No full textThe crystal structure of montanite has been determined using single-crystal X-ray diffraction on a synthetic sample, supported by powder X-ray diffraction (PXRD), electron microprobe analysis (EPMA) and thermogravimetric analyses (TGA). Montanite was first described in 1868 as Bi2TeO6·nH2O (0 ≤ n ≤ 2/3). The determination of the crystal structure of synthetic montanite (refined composition Bi2TeO6·0.22H2O has led to the reassignment of the formula to Bi2TeO6·0.22H2O where 0 ≤ n ≤ 2∕3 rather than the commonly reported Bi2TeO6·2H2O. This change has been accepted by the IMA–CNMNC, Proposal 22-A. The PXRD pattern simulated from the crystal structure of synthetic montanite is a satisfactory match for PXRD scans collected on both historical and recent natural samples, showing their equivalence. Two specimens attributed to the original discoverer of montanite (Frederick A. Genth) from the cotype localities (Highland Mining District, Montana and David Beck’s mine, North Carolina, USA) have been designated as neotypes. Montanite crystallises in space group P6, with the unit-cell parameters a = 9.1195(14) Å, c = 5.5694(8) Å, V = 401.13(14) Å3, and three formula units in the unit cell. The crystal structure of montanite is formed from a framework of BiOn and TeO6 polyhedra. Half of the Bi3+ and all of the Te+ cations are coordinated by six oxygen atoms in trigonal-prismatic arrangements (the first example of this configuration reported for Te6+, while the remaining Bi3+ cations are coordinated by seven O sites. The H2O groups in montanite are structurally incorporated into the network of cavities formed by the three-dimensional framework, with other cavity space occupied by the stereoactive 6s2 lone pair of Bi3+ cations. While evidence for a supercell was observed in synthetic montanite, the subcell refinement of montanite adequately indexes all reflections in the PXRD patterns observed in all natural montanite samples analysed in this study, verifying the identity of montanite as a mineral.Copyright © The Author(s) 2022. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedNHM Repositor
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