Reproducibility: A Researcher-Centered Definition

Recent years have introduced major shifts in scientific reporting and publishing. The scientific community, publishers, funding agencies, and the public expect research to adhere to principles of openness, reproducibility, replicability, and repeatability. However, studies have shown that scientists often have neither the right tools nor suitable support at their disposal to meet these modern science challenges. In fact, even the concrete expectations connected to these terms may be unclear and subject to field-specific, organizational, and personal interpretations. Based on a narrative literature review of work that defines characteristics of open science, reproducibility, replicability, and repeatability, as well as a review of recent work on researcher-centered requirements, we find that the bottom-up practices and needs of researchers contrast top-down expectations encoded in terms related to reproducibility and open science. We identify and define reproducibility as a central term that concerns the ease of access to scientific resources, as well as their completeness, to the degree required for efficiently and effectively interacting with scientific work. We hope that this characterization helps to create a mutual understanding across science stakeholders, in turn paving the way for suitable and stimulating environments, fit to address the challenges of modern science reporting and publishing

Large displays and tablets:Data exploration and its effects on data collection

Data is pivotal to open government initiatives, where citizens are often expected to be informed and actively participate. Yet, it can be difficult for people to understand the meaning of data. Presenting data to the public in an appropriate way may also increase citizen's willingness to participate in data collection. Here we present a study which explores how large screens can support socially relevant data exploration. In a between subject laboratory experiment, we analysed how pairs of participants explored data visualisations on a high-resolution display (LHRD) and a tablet. Our results indicate that LHRDs are less cognitively demanding, while tablets offer more shared control of the interface. Data exploration had limited effect on increasing comfort with sharing personal data but helped increase perceptions of trustworthiness within the data collection process. We observed that appropriately visualised data on either platform has significant potential to increase the public's understanding of large data sets

Gapeau: Enhancing the Sense of Distance to Others with a Head-Mounted Sensor

Human perception lacks the capabilities to accurately assess distance. The recent Covid-19 pandemic outbreak rendered this ability particularly important. Augmenting our sense of distance can help maintain safe separation from others when required. To explore how systems can help users maintain physical distance, we designed, implemented and evaluated Gapeau - a head-mounted system for augmenting the sense of distance. Our system uses proximity sensors and thermal sensing to detect and measure the distance to other people. We conducted a validation protocol, an experiment, in which we compared different feedback modalities, and an in-the-wild study to evaluate Gapeau\u27s performance and suitability for use in social contexts. We found that our system enabled users to more accurately determine whether they were maintaining a safe distance from others. Vibration and auditory feedback were found most effective and usable. Gapeau was perceived as socially acceptable. Our work contributes insights for augmented sensing systems with social relevance

Revisiting Reflection in HCI: Four Design Resources for Technologies that Support Reflection

Reflection is a commonly addressed design goal in commercial systems and in Human-Computer Interaction (HCI) research. Yet, it is still unclear what tools are at the disposal of designers who want to build systems that support reflection. Understanding the design space of reflection support systems and the interaction techniques that can foster reflection is necessary to enable building technologies that contribute to the users\u27 well-being. In order to gain additional insight into how interactive artefacts foster reflection, we investigated past research prototypes and reflection-supporting smartphone applications (apps). Through a structured literature review and an analysis of app reviews, we constructed four design resources for reflection: temporal perspective, conversation, comparison and discovery. We also identified design patterns in past digital artefacts that implement the resources. Our work constitutes intermediate-level knowledge that is intended to inspire future technologies that better support reflection

Intelligent Music Interfaces: When Interactive Assistance and Augmentation Meet Musical Instruments

The interactive augmentation of musical instruments to foster self-expressiveness and learning has a rich history. Over the past decades, the incorporation of interactive technologies into musical instruments emerged into a new research field requiring strong collaboration between different disciplines. The workshop "Intelligent Music Interfaces"consequently covers a wide range of musical research subjects and directions, including (a) current challenges in musical learning, (b) prototyping for improvements, (c) new means of musical expression, and (d) evaluation of the solutions

cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer

<p>Abstract</p> <p>Background</p> <p>Recently published data showed discrepancies beteween <it>P53 </it>cDNA and DNA sequencing in glioblastomas. We hypothesised that similar discrepancies may be observed in other human cancers.</p> <p>Methods</p> <p>To this end, we analyzed 23 colorectal cancers for <it>P53 </it>mutations and gene expression using both DNA and cDNA sequencing, real-time PCR and immunohistochemistry.</p> <p>Results</p> <p>We found <it>P53 </it>gene mutations in 16 cases (15 missense and 1 nonsense). Two of the 15 cases with missense mutations showed alterations based only on cDNA, and not DNA sequencing. Moreover, in 6 of the 15 cases with a cDNA mutation those mutations were difficult to detect in the DNA sequencing, so the results of DNA analysis alone could be misinterpreted if the cDNA sequencing results had not also been available. In all those 15 cases, we observed a higher ratio of the mutated to the wild type template by cDNA analysis, but not by the DNA analysis. Interestingly, a similar overexpression of <it>P53 </it>mRNA was present in samples with and without <it>P53 </it>mutations.</p> <p>Conclusion</p> <p>In terms of colorectal cancer, those discrepancies might be explained under three conditions: 1, overexpression of mutated <it>P53 </it>mRNA in cancer cells as compared with normal cells; 2, a higher content of cells without <it>P53 </it>mutation (normal cells and cells showing <it>K-RAS </it>and/or <it>APC </it>but not <it>P53 </it>mutation) in samples presenting <it>P53 </it>mutation; 3, heterozygous or hemizygous mutations of <it>P53 </it>gene. Additionally, for heterozygous mutations unknown mechanism(s) causing selective overproduction of mutated allele should also be considered. Our data offer new clues for studying discrepancy in <it>P53 </it>cDNA and DNA sequencing analysis.</p

Polymorphic variants of genes involved in homocysteine metabolism in celiac disease

Celiac disease (CD) is a polygenic chronic enteropathy conferring an increased risk for various nutrient deficiency states. Hyperhomocysteinemia is a frequent finding in CD and may be related to the development of venous thrombosis, cardiovascular disease, and stroke in untreated CD patients. Recently, a possible excess in the frequency of the MTHFR c.677C>T (rs1801133) gene variant in CD patients was reported. The purpose of this study was to determine if there exist differences in the distribution of polymorphic variants of genes involved in homocysteine/methyl group metabolism between CD patients and the general population. A set of 10 gene polymorphisms (MTHFR rs1801133, MTR rs1805087, MTHFD1 rs2236225, MTRR rs1801394, CBS 844ins68, BHMT1 rs7356530 and rs3733890, BHMT2 rs526264 and rs625879, and TCN2 rs1801198) was tested in 134 patients with CD and 160 matched healthy controls. The frequency of the MTR rs1805087 GG genotype in CD patients was lower than in controls (0.01 and 0.06, respectively), although statistical significance was not achieved (P = 0.06). For the other analyzed polymorphisms, there was no evidence of difference in both allelic and genotypic distribution between cases and controls. The exhaustive Multifactor Dimensionality Reduction analysis revealed no combination of interactive polymorphisms predicting the incidence of CD. In contrast to the well-documented clinical observations of increased risks of vascular disease in patients with longstanding untreated CD, in our group of patients no significant association with CD was found for all tested polymorphic variants of genes involved in homocysteine metabolism. These findings should be replicated in studies with a larger sample size

An association between polymorphism of the heme oxygenase-1 and -2 genes and age-related macular degeneration

Iron may be implicated in the generation of oxidative stress by the catalyzing the Haber–Weiss or Fenton reaction. On the other hand, oxidative stress has been implicated in the pathogenesis of age-related macular degeneration (AMD) and heme oxygenase-1 (HO-1), encoded by the HMOX1 gene and heme oxygenase-2 (HO-2), encoded by the HMOX2 gene are important markers of iron-related oxidative stress and its consequences. Therefore, variability of the HMOX1 and HMOX2 genes might be implicated in the pathogenesis of AMD through the modulation of the cellular reaction to oxidative stress. In the present work, we investigated the association between AMD and a G → C transversion at the 19 position in the HMOX1 gene (the 19G>C-HMOX1 polymorphism, rs2071747) and a A → G transition at the −42 + 1444 position in the HMOX2 gene (the −42 + 1444A>G-HMOX2 polymorphism, rs2270363) and its modulation by some environmental factors. 279 patients with AMD and 105 controls were recruited in this study and the polymorphisms were typed by restriction fragment length polymorphism and allele-specific polymerase chain reaction (PCR). We observed an association between the occurrence of dry AMD and the G/A genotype of the −42 + 1444A>G-HMOX2 polymorphism (odds ratio (OR) 2.72), whereas the G/G genotype reduced the risk of dry AMD (OR 0.41). The G/C genotype and the C allele of the 19 G>C-HMOX1 polymorphism and the G/G genotype and the G allele of the −42 + 1444A>G-HMOX2 polymorphism were associated with progression of AMD from dry to wet form (OR 4.83, 5.20, 2.55, 1.69, respectively). On the other hand, the G/G genotype and the G allele of the 19 G>C-HMOX1 polymorphism and the A/G genotype and the A allele of the −42 + 1444A>G-HMOX2 polymorphism protected against AMD progression (OR 0.19, 0.19, 0.34, 0.59, respectively). Therefore, the 19G>C-HMOX1 and the −42 + 1444A>G-HMOX2 polymorphisms may be associated with the occurrence and progression of AMD

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18