Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients

Believable conversational agents for teaching ancient history and culture in 3D virtual worlds

University of Technology, Sydney. Faculty of Engineering and Information Technology.This thesis introduces believable conversational agents as an engaging and motivational learning tool for teaching ancient history and culture in virtual worlds. Traditional approaches are lacking engagement, interactivity and socialisation, features that are of tremendous importance to modern students (digital natives). At the same time, modern 3D visualisations primarily focus on the design side of the given space and neglect the actual inhabitants of these ancient places. As a consequence, in such historical or cultural 3D visualisations it is difficult to engage the students in the learning process and to keep track of students' learning progress. Furthermore, this approach neglects the knowledge carriers (inhabitants of the ancient site) which are an important part of a particular culture and played an important role in significant historical events. Embodied conversational agents envisaged by this thesis for teaching ancient history and culture must be believable as they act in highly dynamic and heterogeneous environments such as 3D Virtual Worlds with both human and autonomous agent participants. In these virtual environments participants behave autonomously and frequently interact with each other and with software agents. Therefore, embodied conversational agents must know their surroundings, be aware of their own state in the virtual environment and possess a detailed knowledge of their own interactions as well as the interactions of other participants. We label such agent abilities as "awareness believability" and develop the necessary theoretical background and the formalisation of this concept. We also discuss the I2B (Interactive, Intelligent and Believable) framework that implements awareness believability using the combination of the Virtual Institutions technology, the AIML engine and the visualisation layer of Virtual Worlds. Through a detailed literature review on virtual agents' believability we identified the ability to continuously learn new conversational skills as another important aspect of being believable. Thus, this thesis also explains how AIML specific rules and virtual agents' interactions with subject matter experts help to dynamically improve the conversational corpus of virtual agents via imitation learning. To validate the impact of supplying agents with awareness believability we conducted a number of case studies specific to the domain of ancient history and culture. The studies confirmed that the identified awareness features are indeed making the agents perceived as more believable. Furthermore, the studies provide important evidence in favour of using virtual agents for improving the knowledge of students in the domain of ancient history and culture

The effect of SAHA on the expression of genes in wild type and Hdac2 knockout mouse models and its potential use as treatment for schizophrenia

The symptoms of schizophrenia have been categorized into three subsets including positive, negative, and cognitive symptoms. Although atypical antipsychotic use has shown promising reduction in positive and negative symptoms of schizophrenia, such as hallucination, delusions and flat affect, the cognitive subset of symptoms remains and has an adverse impact on those affected. Chronic treatment with the atypical/secondary antipsychotic clozapine is one example that has ameliorated hallucinations and delusions but results in cognitive memory deficits. When chronically given in conjunction with the HDAC inhibitor, SAHA, the cognitive memory deficits of mouse models decline. HDAC2KO mice were bred and used in chronic treatments with either vehicle or SAHA and compared to WT mice, in order to analyze whether differential gene expression was occurring in an HDAC2 dependent manner. The expression of various genes involved in brain function were evaluated using RT-qPCR to determine potential differential regulation. The results showed differential expression of the following genes: Abhd16a, Gbf1, Itch, and Ube2g1. These genes are all involved in various neuronal functions

An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis. In this paper, we have formulated an automated workflow through which we have identified ontological information, including nutrition-related terms in PubMed abstracts (from 1991 to 2016) for two main types of Inflammatory Bowel Diseases: Crohn’s Disease and Ulcerative Colitis; and two other gastrointestinal (GI) diseases, namely, Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering patterns as well as spatial and temporal trends inherent to the considered GI diseases in terms of literature that has been accumulated so far. Although automated interpretation cannot replace human judgement, the developed workflow shows promising results and can be a useful tool in systematic literature reviews. The workflow is available at https://github.com/KociOrges/pytag

Randomized controlled trials are needed to close the evidence gap in the prevention of preterm birth

Pregnant women have been advised to avoid heavy lifting during pregnancy due to concerns of adverse pregnancy outcomes including premature delivery. To date there is no evidence on the effectiveness of advice in preventing preterm birth as found in a recent systematic search and appraisal of published literature. This letter employs the findings of the review to inform future studies

Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal calprotectin concentrations in children with active Crohn's Disease

No abstract available

A pedestrian path-planning model in accordance with obstacle's danger with reinforcement learning

Most microscopic pedestrian navigation models use the concept of "forces" applied to the pedestrian agents to replicate the navigation environment. While the approach could provide believable results in regular situations, it does not always resemble natural pedestrian navigation behaviour in many typical settings. In our research, we proposed a novel approach using reinforcement learning for simulation of pedestrian agent path planning and collision avoidance problem. The primary focus of this approach is using human perception of the environment and danger awareness of interferences. The implementation of our model has shown that the path planned by the agent shares many similarities with a human pedestrian in several aspects such as following common walking conventions and human behaviours

PHARMGEONETIC EFFECT ON PLASMA CONCENTRATION OF TAMOXIFEN THROUGH HPLC IN FEMALE SUBJECTS OF PAKISTAN

The pharmgeonetic and pharmenzymonetic factors alter plasma concentration of a drug achieved after the same dosage regimen in various individuals. Breast cancer being second most killing disease holds tamoxifen as a treatment of choice for years for woman. Its plasma concentration determines therapeutic output for that eight healthy female volunteers were selected from Pakistan region and single dose 20mg of Tamoxifen was given. After collection of blood samples at known intervals, plasma concentration was determined by high performance liquid chromatography. The maximum plasma concentration was 32.54±0.44 ng/mL at time 6 hours after administration. Mean ± SE initial tamoxifen concentration was 4.8 ± 0.41 ng/mL and at 24 hours it was recorded as 7.4 ± 2.06 ng/mL respectively. The concentration obtained was lesser than literature values proving geographical region dependent decrease altering therapeutic outcome and therapeutic drug monitoring is essential for breast cancer patients in short and for every ailment in long term

Encapsulated virgin coconut oil as a nanoscale in vitro solution against multiple drug resistant Staphylococcus aureus

Abstract Niosomes are excellent nanoscale vehicular systems that can carry a variety of drugs and (bioactive) compounds entrapped inside them. Virgin coconut oil (VCO) is the finest grade of coconut oil that is highly enriched with phenolic content, antioxidant activity and also comprises medium chain triglycerides. In this work, niosomes were encapsulated with VCO synthesized by a simple chemical method. The electron microscopy confirmed that spherical nanostructured lipid carrier molecules with a diameter in the range of 180–190 nm were produced. A zeta potential value of −42 mV was a testimony that these nanovehicles were having good stability. The natural oil loaded nanocarrier spheres proved to be potent antibacterial nano‐antibiotics against multiple drug resistant (MDR) bacteria. The antibacterial activity of these magic nano‐spheres was found to be better than ZnO (metallic oxides) nanoparticles. The nano‐antibiotics resulted in 17, 14 and 12 mm zones of inhibition against methicillin‐resistant Staphylococcus aureus (MRSA), vancomycin‐resistant S. aureus (VRSA) and a (general) MDR strain of S. aureus in contrast to nanoparticles that resulted in zones of inhibitions 7, 8 and 6 mm for the same bacterial strains. Niosomes prove to be an excellent nanocarrier system that can encapsulate a number of bio‐active compounds