Understanding the effects of code presentation

The majority of software is still written using text-based programming languages. With today’s large, high-resolution color displays, developers have devised their own “folk design” methodologies to exploit these advances. As software becomes more and more critical to everyday life, supporting developers in rapidly producing and revising code accurately should be a priority. We consider how layout, typefaces, anti-aliasing, syntax highlighting, and semantic highlighting might impact developer efficiency, and accuracy.This is the author accepted manuscript. The final version is available from the Association for Computing Machinery via http://dx.doi.org/10.1145/2846680.284668

Crowdsourcing design guidance for contextual adaptation of text content in augmented reality

Funding Information: This work was supported by EPSRC (grants EP/R004471/1 and EP/S027432/1). Supporting data for this publication is available at https://doi.org/10.17863/CAM.62931.Augmented Reality (AR) can deliver engaging user experiences that seamlessly meld virtual content with the physical environment. However, building such experiences is challenging due to the developer's inability to assess how uncontrolled deployment contexts may infuence the user experience. To address this issue, we demonstrate a method for rapidly conducting AR experiments and real-world data collection in the user's own physical environment using a privacy-conscious mobile web application. The approach leverages the large number of distinct user contexts accessible through crowdsourcing to efciently source diverse context and perceptual preference data. The insights gathered through this method complement emerging design guidance and sample-limited lab-based studies. The utility of the method is illustrated by reexamining the design challenge of adapting AR text content to the user's environment. Finally, we demonstrate how gathered design insight can be operationalized to provide adaptive text content functionality in an AR headset.Publisher PD

Investigating the accessibility of crowdwork tasks on Mechanical Turk

Funding Information: This work was supported by the EPSRC (grants EP/R004471/1 and EP/S027432/1). Supporting data for this publication is available at https://doi.org/10.17863/CAM.62937.Crowdwork can enable invaluable opportunities for people with disabilities, not least the work fexibility and the ability to work from home, especially during the current Covid-19 pandemic. This paper investigates how engagement in crowdwork tasks is affected by individual disabilities and the resulting implications for HCI. We first surveyed 1,000 Amazon Mechanical Turk (AMT) workers to identify demographics of crowdworkers who identify as having various disabilities within the AMT ecosystem-including vision, hearing, cognition/mental, mobility, reading and motor impairments. Through a second focused survey and follow-up interviews, we provide insights into how respondents cope with crowdwork tasks. We found that standard task factors, such as task completion time and presentation, often do not account for the needs of users with disabilities, resulting in anxiety and a feeling of depression on occasion. We discuss how to alleviate barriers to enable effective interaction for crowdworkers with disabilities.Publisher PD

Metatranscriptome of human faecal microbial communities in a cohort of adult men

The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms\u27 ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic \u27core\u27 universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a \u27variable\u27 metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome

Stability of the human faecal microbiome in a cohort of adult men

Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples—one pair collected 24–72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics

Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men

Background & Aims: Sulfur-metabolizing microbes, which convert dietary sources of sulfur into genotoxic hydrogen sulfide (H2S), have been associated with development of colorectal cancer (CRC). We identified a dietary pattern associated with sulfur-metabolizing bacteria in stool and then investigated its association with risk of incident CRC using data from a large prospective study of men. Methods: We collected data from 51,529 men enrolled in the Health Professionals Follow-up Study since 1986 to determine the association between sulfur-metabolizing bacteria in stool and risk of CRC over 26 years of follow-up. First, in a subcohort of 307 healthy men, we profiled serial stool metagenomes and metatranscriptomes and assessed diet using semiquantitative food frequency questionnaires to identify food groups associated with 43 bacterial species involved in sulfur metabolism. We used these data to develop a sulfur microbial dietary score. We then used Cox proportional hazards modeling to evaluate adherence to this pattern among eligible individuals (n = 48,246) from 1986 through 2012 with risk for incident CRC. Results: Foods associated with higher sulfur microbial diet scores included increased consumption of processed meats and low-calorie drinks and lower consumption of vegetables and legumes. Increased sulfur microbial diet scores were associated with risk of distal colon and rectal cancers, after adjusting for other risk factors (multivariable relative risk, highest vs lowest quartile, 1.43; 95% confidence interval 1.14–1.81; P-trend = .002). In contrast, sulfur microbial diet scores were not associated with risk of proximal colon cancer (multivariable relative risk 0.86; 95% CI 0.65–1.14; P-trend = .31). Conclusions: In an analysis of participants in the Health Professionals Follow-up Study, we found that long-term adherence to a dietary pattern associated with sulfur-metabolizing bacteria in stool was associated with an increased risk of distal CRC. Further studies are needed to determine how sulfur-metabolizing bacteria might contribute to CRC pathogenesis

Global Genetic Population Structure of Bacillus anthracis

Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064–6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated