A basis for the exploration of hypermedia systems : a guided path facility : a thesis presented in partial fulfillment of the requirements for the degree of Master of Arts at Massey University

This thesis examines the potential of a paths facility as an aid to navigating large hypermedia systems. The use of the navigational metaphor as applied to finding information is continued with the idea of following a path through information 'space'. This idea assumes that each node, or chunk of information, on the path can be considered a landmark that can be easily returned to when side-trips are taken off the path to explore the surrounding space. The idea of a guided path assumes the re-use of a path, and also assumes that there is extra information available about the path. This meta-information is very important for providing information to help path-followers make better sense of the path, both in terms of content and context, but also in making more effective use of the nodes on the path and in navigating the variety of interface conventions seen in the test environment - HyperCard. A small pilot study has been carried out using two groups of users performing a directed information-seeking task. One group used HyperCard's navigational facilities to find information in a group of stacks, while the other group used a guided path as a base on which to explore the same group of stacks. Both groups had a time limit, at the end of which they completed a number of questionnaires to indicate task completion, as well as providing a subjective evaluation of the facilities they used. The guided path facility appears to be most effective for inexperienced users for a number of reasons. It presents a simplified view of the complex system - the information available has already been filtered and selected, and a simple and consistent navigational interface reduces the cognitive overheads associated with learning a variety of mechanisms present in different stacks. An important feature of a path facility seems to be the provision of meta-information, especially scope information which can reduce the incidences of disorientation. Another feature is the provision of a history facility which provides a backtracking capability. It may also be used in the creation of paths using the length of visit as a criterion for node inclusion on a new path

Innovative tools and technologies for improving biodiversity surveys using citizen science

This thesis advances knowledge of biodiversity monitoring using citizen science and demonstrates the potential of innovative tools and technology to improve the data generated by citizen science to inform species conservation and ecosystem management. Biodiversity around the world is in crisis and there are many challenges. Australian biodiversity is declining rapidly, with the worst mammal extinction rate in the world. Climate change, pollution, land clearing and other anthropogenic pressures are increasing and exacerbating pressures on ecosystems and wildlife. Biodiversity monitoring is crucial to inform us as to the current state and trends of ecosystems. Resources are limited for traditional scientific monitoring, thus other efficient and effective methods are being sought to augment biodiversity conservation research and management. Effective management solutions require stakeholder engagement, so community participation is one key part of solving this crisis. Citizen science is seen as part of the solution by engaging citizens in local actions that contribute to local and global improved outcomes. However, data contributed by citizen scientists are often seen as biased in space and time, and lacking in essential metadata, such as accurate effort data. The aim of this thesis was to investigate and develop methods to enhance data collected by citizen scientists to improve wildlife monitoring. The objectives were to: 1. assess the potential of automatic collection of key monitoring metadata, such as species location and observer search paths, to enable more accurate assessments of observer effort and species absence; 2. increase knowledge on population distribution and abundance of an iconic Australian mammal species using citizen science and compare spatial coverage of this monitoring to traditional observations, using protected areas and geographic remoteness indicators; 3. assess how CS monitoring performed compared to other forms of monitoring when faced with major disruptions to community activities and movements caused by a global pandemic. These objectives were addressed through three component studies. Firstly, a mobile app was developed which automatically recorded accurate metadata for each observation. Extra information about participants' search effort, including time taken and search path followed, was also automatically recorded. This app was used for a citizen science event to gather information about koala (Phascolarctos cinereus) populations and their habitats in South Australia. Results showed that recording of observations, search effort and search path data was accurate and useful for both species population assessment and management of citizen science monitoring. For objective two, a mobile app was developed to enable citizen scientists across Australia to record observational data and improve knowledge on the iconic short-beaked echidna (Tachyglossus aculeatus). Widespread participation over three years more than doubled observation counts across the continent compared to contemporary scientific observations from national and state repositories, while geographic coverage was similar, except for in some highly protected areas and very remote areas. Finally, citizen science observational data for short-beaked echidna were compared to data from three biodiversity data repositories and demonstrated that citizen science monitoring was resilient to the effects of restrictions on community activities while other forms of monitoring were significantly reduced under harsh restrictions and more concentrated in highly protected areas than usual. This thesis contributes towards efforts to understand and improve citizen science data for monitoring wildlife and biodiversity by enhancing data collection methods. The automatic collection of citizen scientist search paths and effort provides key information about where monitoring has occurred, even without observations being recorded. This is vital information for both modelling species populations and distribution and also for improved management of citizen science monitoring. Baseline echidna population distribution and abundance information has been improved across Australia and will help determine future population trends. This also contributes to our understanding of spatial biases of citizen science and scientific monitoring. Demonstrating the robustness of citizen science monitoring to disruptions caused by restrictions to community activity provides further important knowledge for assessing effective monitoring methods, particularly in light of the current pandemic and ongoing climate change effects. This knowledge will inform management of both CS and scientific biodiversity monitoring and further improve methods for biodiversity conservation in Australia and around the world.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 202

Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs

Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs

A Formação na e para a Pesquisa no PIBID: possibilidades e fragilidades

Ahead of printA Formação na e para a Pesquisa no PIBID: possibilidades e fragilidades. Essa pesquisa objetiva investigar a contribuição do Programa Institucional de Bolsa de Iniciação à Docência (PIBID) para a aprendizagem da docência dos licenciandos, focalizando a construção da identidade docente como professores pesquisadores e reflexivos, no contexto de um Instituto Federal de Ciências, Educação e Tecnologia, por meio de narrativas e análise documental. Evidenciou-se que o PIBID pode se constituir em um espaço de reflexão, em que o formando é incitado a desenvolver postura investigativa, elaborar e executar projeto de ensino e de investigação; entretanto, os estudos e reflexões sobre a pesquisa deve também ser assumido pelos demais professores formadores para que esta atividade seja fortalecida na instituição.The Training in and for Research in PIBID: possibilities and weaknesses. This research aims to investigate contributions of the Programa Institucional de Bolsa de Iniciação a Docência [Institutional Scholar- ship for Teaching Initiation Program] - (PIBID) to the learning of teachers. It is focused on the construction of the professional identity as researchers and reflective teachers, in the context of a Federal Institute of Sciences, Education and Technology, by means of narratives and documents analysis. It was evident that the PIBID may constitute a space for reflection, where the student is encouraged to develop an investigative approach and to prepare and implement educational and research projects; however, studies and reflections concerning research should also be taken by other trainer teachers so that such activity will be strengthened in the institution.CIEC - Centro de Investigação em Estudos da Criança, IE, UMinho (UI 317 da FCT), Portugal; Fundos Nacionais através da FCT (Fundação para a Ciência e a Tecnologia) e cofinanciado pelo Fundo Europeu de Desenvolvimento Regional (FEDER) através do COMPETE 2020 – Programa Operacional Competitividade e Internacionalização (POCI) com a referência POCI-01-0145-FEDER-007562info:eu-repo/semantics/publishedVersio

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Drawing, Outdoor Stage

Watercolor/white paper; 17.5" x 22.5"Part of the Archives' Visual Materials collectio

A Wrought Iron Shop

Ink, watercolor/white paper; 35" x 22.5"EPart of the Archives' Visual Materials collectio