flatIGW - an inverse algorithm to compute the Density of States of lattice Self Avoiding Walks

We show that the Density of States (DoS) for lattice Self Avoiding Walks can be estimated by using an inverse algorithm, called flatIGW, whose step-growth rules are dynamically adjusted by requiring the energy histogram to be locally flat. Here, the (attractive) energy associated with a configuration is taken to be proportional to the number of non-bonded nearest neighbor pairs (contacts). The energy histogram is able to explicitly direct the growth of a walk because the step-growth rule of the Interacting Growth Walk \cite{IGW} samples the available nearest neighbor sites according to the number of contacts they would make. We have obtained the complex Fisher zeros corresponding to the DoS, estimated for square lattice walks of various lengths, and located the $\theta$ temperature by extrapolating the finite size values of the real zeros to their asymptotic value, $\sim 1.49$ (reasonably close to the known value, $\sim 1.50$ \cite{barkema}).Comment: 18 pages, 7 eps figures; parts of the manuscript are rewritten so as to improve clarity of presentation; an extra reference adde

Discourse Semantics for the Analysis of Change in Language

This paper purports to elaborate and address several issues which lie at the intersection of computational linguistics and psychology. The first issue addressed is that of the interaction between discourse and semantics by virtue of empirical linguistic and psychotherapeutic evidence. This paper then gives a formal account of the knowledge representation and reasoning processes involved in the construction of an XML knowledge base for use in the sematic analysis of psychotherapeutic transcripts. Computational methods for the automatic mark-up and inference of the psychotherapeutic phenomena under investigation are detailed in order to further develop intuitions behind a particular pragmatic theory of language known as the Metamodel. The work presented here ultimately aims to produce a sustainable system for the evaluation of the effectiveness of any given psychotherapeutic technique. The possibility exists for such a system to recognise successful therapeutic mechanisms and further still, to infer new ones, or suggest improvements, or offer novel explanations as to the success or failure of the therapy itself. The work discussed here stems from research in computational linguistics, psychotherapy, and philosophy. The corpus used is a culmination of client transcripts taken before, during, and after therapy. The particular therapeutic technique used here is known as the Metamodel (Bandler and Grinder, 1975). The Metamodel was originally proffered as a method of language analysis suitable for use by practitioners of any psychotherapeutic technique. It theorises that speech utterances are related to a clients deep structure through three primary mechanisms, namely generalisation, deletion, and distortion. Previous hand tagging of our data has proven support for such claims. It is our aim to automate the identification and reasoning process. The issues and processes involved in the automation of such tagging are discussed here. Architectural and philosophical issues relating syntax (or grammar), semantics (Larson and Segal, 1995), and pragmatics (Grice, 1989; Searle, 1969) are raised. Discourse Representation Theory (Kamp, 1981; Asher and Lascarides, 1995) is discussed and used here in order to infer discourse relations.Hosted by the Scholarly Text and Imaging Service (SETIS), the University of Sydney Library, and the Research Institute for Humanities and Social Sciences (RIHSS), the University of Sydney

Development of a microsatellite library for the flightless moth Pringleophaga marioni Viette (Lepidoptera: Tineidae)

Fifteen microsatellite markers were isolated from an enriched microsatellite library developed specifically for Pringleophaga marioni, a flightless moth species from the sub-Antarctic Prince Edward Islands. Of these, 12 markers were polymorphic in a population of 44 individuals collected on Marion Island. Between 2 and 7 alleles were amplified per marker and the expected heterozygosities (HE) for these ranged from 0.046 to 0.753. These microsatellite markers reported here are the first for P. marioni and will be used to investigate conservation genetic aspects of this species on the Prince Edward Islands

Molecular and morphometric assessment of the taxonomic status of Ectemnorhinus weevil species (Coleoptera : Curculionidae, Entiminae) from the sub-Antarctic Prince Edward Islands

There are long-standing controversies on the taxonomic status of Ectemnorhinus weevil species occurring on the sub-Antarctic Prince Edward Islands. Since the two islands that constitute the Prince Edward Islands archipelago (PEIA), Marion Island (MI) and Prince Edward Island (PEI), differ in terms of alien invasive species such as the introduced house mouse Mus musculus and conservation management strategies, it is important to consider inter-island dynamics when investigating inter-specific relationships. Using a combined molecular phylogenetic and morphometric approach, we attempted to resolve the taxonomic status of the PEIA Ectemnorhinus weevil species. A COI gene phylogeny was inferred following the genetic characterization of 52 Ectemnorhinus weevils from both islands, and morphometric assessment using a set of 15 linear, external measurements was used to differentiate between the two currently recognized species, Ectemnorhinus similis and Ectemnorhinus marioni. Analyses revealed the presence of two genetically and morphometrically distinct species on PEI, whilst evidence for a single species, comprising diverse genetically discrete populations was found on MI. Based on these results, the species unique to PEI has been designated Ectemnorhinus kuscheli n. sp. whilst we confirm the synonymy between E. similis and E. marioni, the two species originally described from MI. E. kuscheli appears to be restricted to PEI, whereas E. similis occurs on both MI and PEI.Ctr Invas Bio

Plasmodium liver load following parenteral sporozoite administration in rodents

Item does not contain fulltextOne of the bottlenecks in the development of a whole sporozoite malaria vaccine is the route and method of sporozoite administration. Immunization and challenge of human volunteers by mosquito bites is effective, but cannot be used as a vaccine. Intravenous immunization with sporozoites is effective in rodents and non-human primates, and being studied in humans, but is not yet used for licensed vaccines for infectious diseases. Intradermal and subcutaneous immunization regimens show a strong decrease in protective efficacy, which in rodents, is associated with a decreased degree of parasite liver infection during immunization. The objective of this study was to explore alternative routes of sporozoite administration to increase efficiency of liver infection. Using in vivo imaging, we found that IM injection of sporozoites resulted in a greater parasite liver load compared to ID and SC injection. The use of small inoculation volumes and multiple injections further increased the subsequent liver load. These observations were corroborated in a Plasmodium yoelii model using cryopreserved sporozoites administered ID. Our findings provide a rationale for the design of clinical trials to optimize needle and syringe administration of Plasmodium falciparum sporozoites

Assessing the adequacy of attenuation of genetically modified malaria parasite vaccine candidates.

Item does not contain fulltextThe critical first step in the clinical development of a malaria vaccine, based on live-attenuated Plasmodium falciparum sporozoites, is the guarantee of complete arrest in the liver. We report on an approach for assessing adequacy of attenuation of genetically attenuated sporozoites in vivo using the Plasmodium berghei model of malaria and P. falciparum sporozoites cultured in primary human hepatocytes. We show that two genetically attenuated sporozoite vaccine candidates, Deltap52+p36 and Deltafabb/f, are not adequately attenuated. Sporozoites infection of mice with both P. berghei candidates can result in blood infections. We also provide evidence that P. falciparum sporozoites of the leading vaccine candidate that is similarly attenuated through the deletion of the genes encoding the proteins P52 and P36, can develop into replicating liver stages. Therefore, we propose a minimal set of screening criteria to assess adequacy of sporozoite attenuation necessary before advancing into further clinical development and studies in humans

BDES2020 - Decorated Shed <Katherine McCourt>

The prodigious rate at which malaria parasites proliferate during asexual blood-stage replication, midgut sporozoite production, and intrahepatic development creates a substantial requirement for essential nutrients, including fatty acids that likely are necessary for parasite membrane formation. Plasmodium parasites obtain fatty acids either by scavenging from the vertebrate host and mosquito vector or by producing fatty acids de novo via the type two fatty acid biosynthesis pathway (FAS-II). Here, we study the FAS-II pathway in Plasmodium falciparum, the species responsible for the most lethal form of human malaria. Using antibodies, we find that the FAS-II enzyme FabI is expressed in mosquito midgut oocysts and sporozoites as well as liver-stage parasites but not during the blood stages. As expected, FabI colocalizes with the apicoplast-targeted acyl carrier protein, indicating that FabI functions in the apicoplast. We further analyze the FAS-II pathway in Plasmodium falciparum by assessing the functional consequences of deleting fabI and fabB/F. Targeted deletion or disruption of these genes in P. falciparum did not affect asexual blood-stage replication or the generation of midgut oocysts; however, subsequent sporozoite development was abolished. We conclude that the P. falciparum FAS-II pathway is essential for sporozoite development within the midgut oocyst. These findings reveal an important distinction from the rodent Plasmodium parasites P. berghei and P. yoelii, where the FAS-II pathway is known to be required for normal parasite progression through the liver stage but is not required for oocyst development in the Anopheles mosquito midgut

A double-blind, placebo-controlled phase 1/2a trial of the genetically attenuated malaria vaccine PfSPZ-GA1

Immunization with attenuated Plasmodium sporozoites can induce protection against malaria infection, as shown by Plasmodium fakiparum (Pf) sporozoites attenuated by radiation in multiple clinical trials. As alternative attenuation strategy with a more homogeneous population of Pf sporozoites (PfSPZ), genetically engineered Plasmodium berghei sporozoites (SPZ) lacking the genes b9 and slarp induced sterile protection against malaria in mice. Consequently, PfSPZ-GA1 Vaccine, a Pf identical double knockout (Pf Delta b9 Delta s/arp), was generated as a genetically attenuated malaria parasite vaccine and tested for safety, immunogenicity, and preliminary efficacy in malaria-naive Dutch volunteers. Dose-escalation immunizations up to 9.0 x 10(5) PfSPZ of PfSPZ-GA1 Vaccine were well tolerated without break-through blood-stage infection. Subsequently, groups of volunteers were immunized three times by direct venous inoculation with cryopreserved PfSPZ-GA1 Vaccine (9.0 x 10(5) or 4.5 x 10(5) PfSPZ, N = 13 each), PfSPZ Vaccine (radiation-attenuated PfSPZ, 4.5 x 10(5) PfSPZ, N= 13), or normal saline placebo at 8-week intervals, followed by exposure to mosquito bite controlled human malaria infection (CHMI). After CHMI, 3 of 25 volunteers from both PfSPZ-GA1 groups were sterilely protected, and the remaining 17 of 22 showed a patency >= 9 days (median patency in controls, 7 days; range, 7 to 9). All volunteers in the PfSPZ Vaccine control group developed parasitemia (median patency, 9 days; range, 7 to 12). Immunized groups exhibited a significant, dose-related increase in anti-Pf circumsporozoite protein (CSP) antibodies and Pf-specific interferon-gamma (IFN-gamma)-producing T cells. Although no definite conclusion can be drawn on the potential strength of protective efficacy of PfSPZ-GA1 Vaccine, the favorable safety profile and induced immune responses by PfSPZ-GA1 Vaccine warrant further clinical evaluation.Medical Microbiolog