Towards the Humanisation of Programming Tool Interactions

Program analysis tools, from simple static semantic analysis by a compiler, to complex dynamic analyses of data flow and security, have become commonplace in modern day programming. Many of the simpler analyses, such as the afore- mentioned compiler checking or linters designed to enforce code style, may even go unnoticed or unconsidered by most users, ubiquitous as they are. Despite this, and despite the obvious utility that such programming tools can provide, many warnings provided by them go unheeded by programmers most of the time.There are several reasons for this phenomenon: the propensity to produce false positives undermines confidence in the validity of warnings, the tools do not in- tegrate well into the normal workflow of the developer, sometimes the warning message is simply too esoteric for most users to understand, and so on. A com- mon theme can be drawn from these reasons for ignoring the often-times very useful information given by a programming tool: the tool itself is difficult to use.In this thesis, we consider ways in which we can bridge this gap between users and tools. To do this, we draw from observations about the way in which we interact with each other in the most basic human-to-human context. Applying these lessons to a human-tool interaction allow us to examine ways in which tools may be deficient, and investigate methods for making the interaction more natural and human-like.We explore this issue by framing the interaction as a "conversation" between a human and their development environment. We then present a new programming tool, Progger, built using design principles driven by the "conversational lens" which we use to look at these interactions. After this, we present a user study using a novel low-cost methodology, aimed at evaluating the efficacy of the Progger tool. From the results of this user study, we present a new, more streamlined version of Progger, and finally investigate the way in which it can be used to direct the users attention when conducting a code comprehension exercise

A Pilot Study of Value of Information Analysis to Support Research Recommendations for the National Institute for Health and Clinical Excellence

Background - This project developed as a result of the activities of the Research Teams at the Centre for Health Economics, University of York, and ScHARR at the University of Sheffield in the methods and application of decision analysis and value of information analysis as a means of informing the research recommendations made by NICE, as part of its Guidance to the NHS in England and Wales, and informing the deliberations of the NICE Research and Development Committee. Objectives - The specific objectives of the pilot study were to: • Demonstrate the benefits of using appropriate decision analytic methods and value of information analysis to inform research recommendations. • Establish the feasibility and resource implications of applying these methods in a timely way, to inform NICE. • Identify critical issues and methodological challenges to the use of value of information methods for research recommendations (with particular regard to the new reference case as a suitable basis for this type of analysis).

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

peer-reviewedMethane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal’s compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH4 mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management

The practice and regulatory requirements of naturopathy and western herbal medicine in Australia

Australian health workforce regulation is premised on the need to protect public health and safety. Specific criteria are set out by governments to ascertain the degree of risk and the need for government intervention. A study was undertaken to understand the current state of usage and the practice of naturopathy and western herbal medicine, and to ascertain whether statutory regulation was warranted. We found increased use of these complementary therapies in the community, with risks arising from both the specific practices as well as consumers negotiating a parallel primary health care system. We also found highly variable standards of training, a myriad of professional associations, and a general failure of current systems of self-regulation to protect public health and safety. Statutory regulation was the preferred policy response for consumers, insurers, general practitioners, and most of the complementary therapists. While we found a case for statutory registration, we also argue that a minimalist regulatory response needs to be accompanied by other measures to educate the public, to improve the standards of practice, and to enhance our understanding of the interaction between complementary and mainstream health care

Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle

peer-reviewedCompensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is exploited worldwide in animal production systems as a method to lower feed costs. However the molecular mechanisms regulated CG expression remain to be elucidated fully. This study aimed to uncover the underlying biology regulating CG in cattle, through an examination of skeletal muscle transcriptional profiles utilising next generation mRNA sequencing technology. Twenty Holstein Friesian bulls were fed either a restricted diet for 125 days, with a target growth rate of 0.6 kg/day (Period 1), following which they were allowed feed ad libitum for a further 55 days (Period 2) or fed ad libitum for the entirety of the trial. M. longissimus dorsi biopsies were harvested from all bulls on days 120 and 15 of periods 1 and 2 respectively and RNAseq analysis was performed. During realimentation in Period 2, previously restricted animals displayed CG, growing at 1.8 times the rate of the ad libitum control animals. Compensating animals were also more feed efficient during re-alimentation and compensated for 48% of their previous dietary restriction. 1,430 and 940 genes were identified as significantly differentially expressed (Benjamini Hochberg adjusted P < 0.1) in periods 1 and 2 respectively. Additionally, 2,237 genes were differentially expressed in animals undergoing CG relative to dietary restriction. Dietary restriction in Period 1 was associated with altered expression of genes involved in lipid metabolism and energy production. CG expression in Period 2 occurred in association with greater expression of genes involved in cellular function and organisation. This study highlights some of the molecular mechanisms regulating CG in cattle. Differentially expressed genes identified are potential candidate genes for the identification of biomarkers for CG and feed efficiency, which may be incorporated into future breeding programme

Screening of siRNA Nanoparticles for Delivery to Airway Epithelial Cells Using High Content Analysis

Background: Delivery of siRNA to the lungs via inhalation offers a unique opportunity to develop novel methods of treating a range of poorly treated respiratory conditions. However progress has been greatly hindered by safety and delivery issues. This study developed a high-throughput method for screening novel nanotechnologies for pulmonary siRNA delivery Methodology: Following physico-chemical analysis, the ability of PEI-PEG/siRNA nanoparticles to facilitate siRNA delivery was determined using high content analysis (HCA) in Calu-3 cells. Results obtained from HCA were validated using confocal microscopy. Finally, cytotoxicity of the PEI-PEG/siRNA particles was analysed by HCA using the Cellomics® multiparamter cytotoxicity assay. Conclusions: PEI-PEG/siRNA nanoparticles facilitated increased siRNA uptake and luciferase knockdown in Calu-3 cells compared to PEI/siRNA

Absence of Antisperm Antibodies in Anejaculatory Men

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96435/1/j.1939-4640.1990.tb00162.x.pd

Stable water isotope and surface heat flux simulation using ISOLSM: Evaluation against in-situ measurements

Author's manuscript made available in accordance with the publisher's policy.The stable isotopes of water are useful tracers of water sources and hydrological processes. Stable water isotope-enabled land surface modeling is a relatively new approach for characterizing the hydrological cycle, providing spatial and temporal variability for a number of hydrological processes. At the land surface, the integration of stable water isotopes with other meteorological measurements can assist in constraining surface heat flux estimates and discriminate between evaporation (E) and transpiration (T). However, research in this area has traditionally been limited by a lack of continuous in-situ isotopic observations. Here, the National Centre for Atmospheric Research stable isotope-enabled Land Surface Model (ISOLSM) is used to simulate the water and energy fluxes and stable water isotope variations. The model was run for a period of one month with meteorological data collected from a coastal sub-tropical site near Sydney, Australia. The modeled energy fluxes (latent heat and sensible heat) agreed reasonably well with eddy covariance observations, indicating that ISOLSM has the capacity to reproduce observed flux behavior. Comparison of modeled isotopic compositions of evapotranspiration (ET) against in-situ Fourier Transform Infrared spectroscopy (FTIR) measured bulk water vapor isotopic data (10 m above the ground), however, showed differences in magnitude and temporal patterns. The disparity is due to a small contribution from local ET fluxes to atmospheric boundary layer water vapor (∼1% based on calculations using ideal gas law) relative to that advected from the ocean for this particular site. Using ISOLSM simulation, the ET was partitioned into E and T with 70% being T. We also identified that soil water from different soil layers affected T and E differently based on the simulated soil isotopic patterns, which reflects the internal working of ISOLSM. These results highlighted the capacity of using the isotope-enabled models to discriminate between different hydrological components and add insight into expected hydrological behavior