title: An investigation of a Mollicute-like organism inhabiting the human gastrointestinal tract

authors: Care, Andrew Shane

subjects: Mollicute

abstract: The microflora inhabiting the human gastrointestinal tract can be considered an essential 'metabolic organ', in a symbiotic relationship with its host. Due to the low cultivability and inappropriate sampling methodology the microflora is poorly explored and ill-defined. 

Preliminary, molecular-based research at the University of Waikato revealed the presence of 16S rRNA gene sequences originating from novel Mollicute-like species inhabiting the human GI tract. A ~830bp 'consensus' sequence representing these novel Mollicute-like sequences was classified within the Mollicute Genus Anaeroplasma the type species of which is Anaeroplasma abactoclasticum. It also displayed near exact matches with 16S rRNA sequences obtained from the human GI tract and matches of high similarity to those from the mouse GI tract in the NCBI database.

This thesis describes an attempt to design and create primers that would amplify and characterize full-length versions of these Mollicute-like sequences from samples obtained from the mucosal surface of the human gastrointestinal tract. Primers sets targeted extended 5' and 3' versions of these novel 'known' sequences and were designed from sequence matches found in the preliminary work and other related sequences from the NCBI database.

The attempt to amplify a full-length version of these novel Mollicute-like sequences was proven to be unsuccessful. No sequences were classified within the Genus Anaeroplasma, although 81% of amplicons from the 5' extending primer sets were classified within the same division as the Mollicutes, the Firmicutes, only 6% of the sequenced amplicons from the 3' extending primer set belonged to this division. Phylograms containing these 'relevant' sequences and the 'consensus' sequence grouped the 'consensus' sequence separately, indicating a lower relatedness than would have been seen if any of the amplicons contained the 'consensus' sequence.

text: An investigation of a Mollicute-like organism inhabiting the human gastrointestinal tract The microflora inhabiting the human gastrointestinal tract can be considered an essential 'metabolic organ', in a symbiotic relationship with its host. Due to the low cultivability and inappropriate sampling methodology the microflora is poorly explored and ill-defined. 

Preliminary, molecular-based research at the University of Waikato revealed the presence of 16S rRNA gene sequences originating from novel Mollicute-like species inhabiting the human GI tract. A ~830bp 'consensus' sequence representing these novel Mollicute-like sequences was classified within the Mollicute Genus Anaeroplasma the type species of which is Anaeroplasma abactoclasticum. It also displayed near exact matches with 16S rRNA sequences obtained from the human GI tract and matches of high similarity to those from the mouse GI tract in the NCBI database.

This thesis describes an attempt to design and create primers that would amplify and characterize full-length versions of these Mollicute-like sequences from samples obtained from the mucosal surface of the human gastrointestinal tract. Primers sets targeted extended 5' and 3' versions of these novel 'known' sequences and were designed from sequence matches found in the preliminary work and other related sequences from the NCBI database.

The attempt to amplify a full-length version of these novel Mollicute-like sequences was proven to be unsuccessful. No sequences were classified within the Genus Anaeroplasma, although 81% of amplicons from the 5' extending primer sets were classified within the same division as the Mollicutes, the Firmicutes, only 6% of the sequenced amplicons from the 3' extending primer set belonged to this division. Phylograms containing these 'relevant' sequences and the 'consensus' sequence grouped the 'consensus' sequence separately, indicating a lower relatedness than would have been seen if any of the amplicons contained the 'consensus' sequence.

year: 2009

title: Using task models to understand the intersection of numeracy skills and technical competence with medical device design

authors: Bowen, Judy

abstract: Task models are used in many different ways throughout the design and development of interactive systems. When the interactive systems are safety critical, task models can play an important role in ensuring system behaviours are consistent with user requirements, which may help to prevent errors. While task models can be used to describe a user’s goals and the steps required to achieve that goal, to understand where user errors may occur we also need to consider the users’ understanding of how to perform a task and how this relates to the system they are using. Our focus is on the use of medical devices such as syringe drivers and infusion pumps for intravenous medication, which forms a major part of hospital inpatient care throughout the world. While we might rely on software engineering and human factors techniques to ensure correctness of such devices, their use by medical personnel in practice includes other factors that are equally important. These include training medical personnel in the use of medical devices. Also numeracy education for medical staff to ensure that they are able to set up and perform the necessary calculations to convert prescribed medication into the appropriate values and measures for their delivery mechanisms. We have developed an approach that aims to bring together concepts of technology design (both functional correctness and usability concerns), numeracy and medication delivery competency. In order to do so we use task models as a common language that enables us to consider these different domains in a single way. We find that the ability to describe the two domains within a single process allows us to compare models of knowledge, tasks and use of devices, which can elicit potential mismatches and problems.

text: Using task models to understand the intersection of numeracy skills and technical competence with medical device design Task models are used in many different ways throughout the design and development of interactive systems. When the interactive systems are safety critical, task models can play an important role in ensuring system behaviours are consistent with user requirements, which may help to prevent errors. While task models can be used to describe a user’s goals and the steps required to achieve that goal, to understand where user errors may occur we also need to consider the users’ understanding of how to perform a task and how this relates to the system they are using. Our focus is on the use of medical devices such as syringe drivers and infusion pumps for intravenous medication, which forms a major part of hospital inpatient care throughout the world. While we might rely on software engineering and human factors techniques to ensure correctness of such devices, their use by medical personnel in practice includes other factors that are equally important. These include training medical personnel in the use of medical devices. Also numeracy education for medical staff to ensure that they are able to set up and perform the necessary calculations to convert prescribed medication into the appropriate values and measures for their delivery mechanisms. We have developed an approach that aims to bring together concepts of technology design (both functional correctness and usability concerns), numeracy and medication delivery competency. In order to do so we use task models as a common language that enables us to consider these different domains in a single way. We find that the ability to describe the two domains within a single process allows us to compare models of knowledge, tasks and use of devices, which can elicit potential mismatches and problems.

year: 2021

title: COVID-19 and blind spaces: Responding to digital (in)accessibility and social isolation during lockdown for blind, deafblind, low vision, and vision impaired persons in Aotearoa New Zealand

authors: Graham, Rebekah Sarah

abstract: In this chapter we, as Indigenous (Māori) and non-Indigenous (Pākehā) academics, practitioners, and disability advocates critically examine the experiences of people who are blind, deafblind, low vision and vision impaired (BLV) during the COVID-19 lockdown of Aotearoa New Zealand. We pay particular attention to the ways in which access (or lack thereof) to digital spaces facilitated experiences of social inclusion (and exclusion). Digital connectivity was heavily relied upon during lockdown in Aotearoa New Zealand to disseminate health information and to connect people socially. The use of digital technologies during lockdown extended the interpersonal space of the home beyond the physicality of the urban home people were confined to, drawing people together across the country and creating a sense of shared experience. However, these experiences were not shared equally across the citizenry. Conversations during lockdown with disability advocates and practitioners working with BLV persons identified that. For example, the government website on COVID19 was initially inaccessible for BLV persons and there were assumptions of digital accessibility and literacy within the domestic space of the home. Taken together, these exacerbated existing inequities for BLV persons, some of whom experience multiple domains of exclusion (for example, Indigenous BLV persons with reduced access to services and for whom English is their second language). Drawing on Lefebvre’s (1991) work on the dialectics of space and Lewin’s (1936/2013) construction of the life-space, we consider the interplay of space and experience with regards to the digital and physical space(s) available and inhabited during the shared social experience of lockdown. We discuss possibilities for co-creating socially inclusive (digital) spaces of belonging that reflect and refract life-space relational connections across social groups. Our reflections on the lockdown experience include opportunities post-pandemic for policy makers and practitioners to address digital accessibility inequities.

text: COVID-19 and blind spaces: Responding to digital (in)accessibility and social isolation during lockdown for blind, deafblind, low vision, and vision impaired persons in Aotearoa New Zealand In this chapter we, as Indigenous (Māori) and non-Indigenous (Pākehā) academics, practitioners, and disability advocates critically examine the experiences of people who are blind, deafblind, low vision and vision impaired (BLV) during the COVID-19 lockdown of Aotearoa New Zealand. We pay particular attention to the ways in which access (or lack thereof) to digital spaces facilitated experiences of social inclusion (and exclusion). Digital connectivity was heavily relied upon during lockdown in Aotearoa New Zealand to disseminate health information and to connect people socially. The use of digital technologies during lockdown extended the interpersonal space of the home beyond the physicality of the urban home people were confined to, drawing people together across the country and creating a sense of shared experience. However, these experiences were not shared equally across the citizenry. Conversations during lockdown with disability advocates and practitioners working with BLV persons identified that. For example, the government website on COVID19 was initially inaccessible for BLV persons and there were assumptions of digital accessibility and literacy within the domestic space of the home. Taken together, these exacerbated existing inequities for BLV persons, some of whom experience multiple domains of exclusion (for example, Indigenous BLV persons with reduced access to services and for whom English is their second language). Drawing on Lefebvre’s (1991) work on the dialectics of space and Lewin’s (1936/2013) construction of the life-space, we consider the interplay of space and experience with regards to the digital and physical space(s) available and inhabited during the shared social experience of lockdown. We discuss possibilities for co-creating socially inclusive (digital) spaces of belonging that reflect and refract life-space relational connections across social groups. Our reflections on the lockdown experience include opportunities post-pandemic for policy makers and practitioners to address digital accessibility inequities.

year: 2021