title: Collaborative, integrated software development with multiple views

authors: Grundy, John C.

subjects: computer science

abstract: This paper presents a new model for supporting collaborative, integrated software development utilising multiple textual and graphical views. Views can be asynchronously edited by different developers using separate versions. Versions can be incrementally merged, with merge conflicts detected and presented. Synchronous editing of views by different developers is also supported. View updates are broadcast to other users and are incrementally incorporated as required in their alternative versions. The new model is illustrated by its use in a software development environment for an object-oriented language.

text: Collaborative, integrated software development with multiple views This paper presents a new model for supporting collaborative, integrated software development utilising multiple textual and graphical views. Views can be asynchronously edited by different developers using separate versions. Versions can be incrementally merged, with merge conflicts detected and presented. Synchronous editing of views by different developers is also supported. View updates are broadcast to other users and are incrementally incorporated as required in their alternative versions. The new model is illustrated by its use in a software development environment for an object-oriented language.

year: 1994-05

title: Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

authors: Lee, Charles Kai-Wu

subjects: RNA 16S

abstract: Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

text: Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

year: 2012

title: Health equity and wellbeing among older people's caregivers in New Zealand during COVID-19: Protocol for a qualitative study.

authors: Burholt, Vanessa

subjects: Aged

abstract: BACKGROUND: Knowledge of the challenges unpaid caregivers faced providing care to older people during the COVID-19 pandemic is limited. Challenges may be especially pronounced for those experiencing inequitable access to health and social care. This participatory action research study, located in New Zealand, has four main objectives, (i) to understand the challenges and rewards associated with caregiving to older care recipients during the COVID-19 pandemic restrictions; (ii) to map and collate resources developed (or mobilised) by organisations during the pandemic; (iii) to co-produce policy recommendations, identify useful caregiver resources and practices, prioritise unmet needs (challenges); and, (iv) to use project results in knowledge translation, in order to improve caregivers access to resources, and raise the profile and recognition of caregivers contribution to society. METHODS AND ANALYSIS: Māori, Pacific and rural-dwelling caregivers to 30 older care-recipients, and 30 representatives from organisations supporting caregivers in New Zealand will be interviewed. Combining data from the interviews and caregivers letters (from an archive of older people's pandemic experiences), framework analysis will be used to examine the interrelated systems of the human ecological model and the impact on caregiving experiences during the pandemic. Resources that service providers had created or used for caregivers and older people will be collated and categorised. Through co-production with caregivers and community partners we will produce three short films describing caregivers' pandemic experiences; identify a suite of resources for caregivers to use in future events requiring self-isolation, and in everyday life; and generate ideas to address unresolved issues.

text: Health equity and wellbeing among older people's caregivers in New Zealand during COVID-19: Protocol for a qualitative study. BACKGROUND: Knowledge of the challenges unpaid caregivers faced providing care to older people during the COVID-19 pandemic is limited. Challenges may be especially pronounced for those experiencing inequitable access to health and social care. This participatory action research study, located in New Zealand, has four main objectives, (i) to understand the challenges and rewards associated with caregiving to older care recipients during the COVID-19 pandemic restrictions; (ii) to map and collate resources developed (or mobilised) by organisations during the pandemic; (iii) to co-produce policy recommendations, identify useful caregiver resources and practices, prioritise unmet needs (challenges); and, (iv) to use project results in knowledge translation, in order to improve caregivers access to resources, and raise the profile and recognition of caregivers contribution to society. METHODS AND ANALYSIS: Māori, Pacific and rural-dwelling caregivers to 30 older care-recipients, and 30 representatives from organisations supporting caregivers in New Zealand will be interviewed. Combining data from the interviews and caregivers letters (from an archive of older people's pandemic experiences), framework analysis will be used to examine the interrelated systems of the human ecological model and the impact on caregiving experiences during the pandemic. Resources that service providers had created or used for caregivers and older people will be collated and categorised. Through co-production with caregivers and community partners we will produce three short films describing caregivers' pandemic experiences; identify a suite of resources for caregivers to use in future events requiring self-isolation, and in everyday life; and generate ideas to address unresolved issues.

year: 2022